Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbl Working: n-0-139.cluster.ucsf.bkslab.org:/scratch/xiaobo/11891/xbl-8058088.38 Result: /scratch/xiaobo/11891/xbl-8058088.38 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbl 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/xbl mkdir: created directory `/scratch/xiaobo/11891' mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38' /scratch/xiaobo/11891/xbl-8058088.38 /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/11891/xbl-8058088.38/working' mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/protonate' Storing results in /scratch/xiaobo/11891/xbl-8058088.38/finished Working in /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 /scratch/xiaobo/11891/xbl-8058088.38/working/protonate /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Using inputs as protomers/tautomers. No processing done 467 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/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Bulk generating 3D conformations all protomers in /scratch/xiaobo/11891/xbl-8058088.38/working/3D mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/11891/xbl-8058088.38/working/protonate/xbl-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 ZINC001566196085 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building' mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001566196085 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/1 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)ccc1NC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566196085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566196085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001566196085 none O=C(Nc1cc(Br)ccc1NC1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 17, 1, 1, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 13, 13, 13, 9, 13, 13, 13, 21, 36, 36, 1, 1, 1, 10, 10, 10, 10, 10, 4, 13, 13, 13, 21, 36, 36, 36, 36, 36, 10, 10] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566196085 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/finished' Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196085 Building ZINC001566196168 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566196168 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/2 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566196168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566196168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001566196168 none CC(C)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 10, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 43, 33, 10, 10, 10, 4, 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]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/3 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566196168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566196168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001566196168 none CC(C)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 9, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 43, 33, 9, 9, 9, 4, 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]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566196168 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 Building ZINC001566196168 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566196168 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 2) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566196168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566196168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001566196168 none CC(C)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 10, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 43, 33, 10, 10, 10, 4, 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]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 3) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566196168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566196168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001566196168 none CC(C)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 9, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 43, 43, 43, 43, 43, 43, 43, 33, 9, 9, 9, 4, 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]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566196168 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566196168 Building ZINC001566210484 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566210484 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/4 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566210484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210484 none O=C(N1CCC[C@@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 16, 16, 16, 16, 16, 16, 26, 26, 16, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/5 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566210484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210484 none O=C(N1CCC[C@@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 17, 17, 17, 17, 17, 17, 27, 27, 23, 27, 27, 27, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566210484 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 Building ZINC001566210484 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566210484 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 4) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566210484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210484 none O=C(N1CCC[C@@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 16, 16, 16, 16, 16, 16, 26, 26, 16, 26, 26, 26, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 26, 26, 26, 26, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 5) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566210484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210484 none O=C(N1CCC[C@@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 17, 17, 17, 17, 17, 17, 27, 27, 23, 27, 27, 27, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566210484 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210484 Building ZINC001566210485 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566210485 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/6 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566210485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210485 none O=C(N1CCC[C@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 18, 18, 18, 18, 18, 18, 31, 31, 25, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/7 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566210485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210485 none O=C(N1CCC[C@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566210485 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 Building ZINC001566210485 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566210485 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 6) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566210485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210485 none O=C(N1CCC[C@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 18, 18, 18, 18, 18, 18, 31, 31, 25, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 31, 31, 31, 31, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 7) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001566210485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566210485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001566210485 none O=C(N1CCC[C@H]1c1ccc(Br)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 11, 11] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566210485 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566210485 Building ZINC001566246729 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566246729 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/8 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1) `ZINC001566246729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001566246729 none Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', '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', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 26, 26, 26, 26, 26, 26, 7, 7, 7, 3, 6, 6, 6, 6, 26, 26, 26, 26] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/9 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1) `ZINC001566246729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001566246729 none Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', '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', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 26, 26, 17, 26, 26, 26, 7, 7, 7, 3, 6, 6, 6, 6, 26, 26, 25, 26] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566246729 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 Building ZINC001566246729 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566246729 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 8) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1) `ZINC001566246729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001566246729 none Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', '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', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 26, 26, 26, 26, 26, 26, 7, 7, 7, 3, 6, 6, 6, 6, 26, 26, 26, 26] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 9) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1) `ZINC001566246729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566246729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001566246729 none Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', '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', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 26, 26, 17, 26, 26, 26, 7, 7, 7, 3, 6, 6, 6, 6, 26, 26, 25, 26] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566246729 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566246729 Building ZINC001566313239 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566313239 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/10 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566313239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313239 none Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/11 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566313239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313239 none Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 31, 33, 33, 15, 15, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 31, 31, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566313239 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 Building ZINC001566313239 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566313239 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 10) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566313239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313239 none Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 11) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566313239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313239 none Cc1nn(CC(C)C)c(Cl)c1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 31, 33, 33, 15, 15, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 31, 31, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566313239 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313239 Building ZINC001566313240 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566313240 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/12 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566313240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313240 none Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 32, 32, 16, 16, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 31, 31, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/13 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566313240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313240 none Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 30, 30, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566313240 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 Building ZINC001566313240 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566313240 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 12) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566313240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313240 none Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 32, 32, 16, 16, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 31, 31, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 13) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001566313240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566313240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001566313240 none Cc1nn(CC(C)C)c(Cl)c1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 30, 30, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 29, 29, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566313240 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566313240 Building ZINC001566317607 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566317607 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/14 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566317607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317607 none CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 33, 33, 44, 26, 33, 12, 11, 15, 15, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 15, 15, 6, 6, 6, 4, 3, 1, 3, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/15 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566317607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317607 none CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 30, 31, 41, 24, 30, 6, 6, 14, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 14, 14, 6, 6, 6, 3, 3, 1, 3, 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]) total number of confs: 260 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566317607 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 Building ZINC001566317607 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566317607 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 14) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566317607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317607 none CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 33, 33, 44, 26, 33, 12, 11, 15, 15, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 15, 15, 6, 6, 6, 4, 3, 1, 3, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 256 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 15) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566317607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317607 none CCN(CC)C(=O)Nc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 30, 31, 41, 24, 30, 6, 6, 14, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 14, 14, 6, 6, 6, 3, 3, 1, 3, 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]) total number of confs: 260 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566317607 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317607 Building ZINC001566317608 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566317608 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/16 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566317608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317608 none CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 30, 31, 41, 24, 30, 12, 6, 14, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 14, 14, 6, 6, 6, 3, 3, 1, 3, 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]) total number of confs: 262 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/17 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566317608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317608 none CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 32, 32, 32, 43, 26, 32, 12, 6, 15, 15, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 15, 15, 6, 6, 6, 4, 3, 1, 3, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566317608 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 Building ZINC001566317608 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566317608 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 16) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566317608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317608 none CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 30, 31, 41, 24, 30, 12, 6, 14, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 24, 14, 14, 6, 6, 6, 3, 3, 1, 3, 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]) total number of confs: 262 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 17) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001566317608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566317608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001566317608 none CCN(CC)C(=O)Nc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 32, 32, 32, 43, 26, 32, 12, 6, 15, 15, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 26, 15, 15, 6, 6, 6, 4, 3, 1, 3, 15, 15] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 270 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566317608 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566317608 Building ZINC001566656208 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566656208 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/18 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566656208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656208 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 9, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 4, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/19 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566656208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656208 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 25, 25, 25, 25, 49, 49, 50, 50, 49, 50, 50, 49, 50, 50, 50, 50, 50, 50, 25, 25, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 3, 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]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566656208 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 Building ZINC001566656208 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566656208 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 18) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566656208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656208 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 9, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 4, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 19) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566656208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656208 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 25, 25, 25, 25, 49, 49, 50, 50, 49, 50, 50, 49, 50, 50, 50, 50, 50, 50, 25, 25, 3, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 3, 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]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566656208 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656208 Building ZINC001566656209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566656209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/20 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566656209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656209 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 5, 9, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 26, 26, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 4, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/21 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566656209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656209 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 10, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 3, 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]) total number of confs: 168 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566656209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 Building ZINC001566656209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566656209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 20) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566656209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656209 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 5, 9, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 26, 26, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 4, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 21) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1) `ZINC001566656209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566656209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001566656209 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 5, 10, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 3, 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]) total number of confs: 168 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566656209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566656209 Building ZINC001566933497 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566933497 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/22 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566933497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933497 none Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 18, 7, 18, 18, 28, 28, 3, 7, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/23 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566933497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933497 none Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 15, 7, 15, 15, 25, 25, 4, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566933497 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 Building ZINC001566933497 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566933497 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 22) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566933497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933497 none Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 18, 7, 18, 18, 28, 28, 3, 7, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 23) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566933497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933497 none Cc1cc(Br)cc2cc([C@@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 15, 7, 15, 15, 25, 25, 4, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566933497 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933497 Building ZINC001566933498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566933498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/24 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566933498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933498 none Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 16, 7, 16, 16, 25, 25, 4, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/25 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566933498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933498 none Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 17, 7, 17, 17, 27, 27, 3, 7, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566933498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 Building ZINC001566933498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566933498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 24) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566933498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933498 none Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 16, 7, 16, 16, 25, 25, 4, 7, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 25) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21) `ZINC001566933498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566933498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001566933498 none Cc1cc(Br)cc2cc([C@H](C(C)C)N(C)C(=O)[C@]([O-])([SiH3])c3cccn3C)oc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 17, 7, 17, 17, 27, 27, 3, 7, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001566933498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001566933498 Building ZINC001567471346 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567471346 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/26 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567471346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471346 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 11, 14, 14, 11, 14, 14, 5, 10, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 2, 6, 6, 11, 11, 14, 14, 11, 14, 14, 10, 10, 39, 17, 17, 17, 17, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/27 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567471346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471346 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 10, 10, 9, 10, 10, 3, 6, 10, 10, 10, 15, 15, 10, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 6, 6, 10, 10, 10, 10, 10, 6, 6, 30, 15, 15, 10, 15, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567471346 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 Building ZINC001567471346 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567471346 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 26) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567471346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471346 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 11, 14, 14, 11, 14, 14, 5, 10, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 2, 6, 6, 11, 11, 14, 14, 11, 14, 14, 10, 10, 39, 17, 17, 17, 17, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 27) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567471346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471346 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 10, 10, 9, 10, 10, 3, 6, 10, 10, 10, 15, 15, 10, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 6, 6, 10, 10, 10, 10, 10, 6, 6, 30, 15, 15, 10, 15, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567471346 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471346 Building ZINC001567471347 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567471347 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/28 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567471347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471347 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 1, 1, 2, 5, 9, 9, 6, 9, 9, 2, 5, 10, 10, 10, 15, 15, 14, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 2, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 5, 30, 15, 15, 14, 15, 5] 150 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]) total number of confs: 140 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/29 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567471347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471347 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 12, 15, 15, 14, 15, 15, 5, 10, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 2, 6, 6, 12, 12, 15, 15, 15, 15, 15, 10, 10, 42, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567471347 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 Building ZINC001567471347 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567471347 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 28) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567471347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471347 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 2, 5, 5, 1, 1, 1, 1, 1, 1, 2, 5, 9, 9, 6, 9, 9, 2, 5, 10, 10, 10, 15, 15, 14, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 2, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 5, 30, 15, 15, 14, 15, 5] 150 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]) total number of confs: 140 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 29) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)c1) `ZINC001567471347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567471347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001567471347 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 12, 15, 15, 14, 15, 15, 5, 10, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 2, 6, 6, 12, 12, 15, 15, 15, 15, 15, 10, 10, 42, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567471347 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567471347 Building ZINC001567497627 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567497627 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/30 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1) `ZINC001567497627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567497627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001567497627 none CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 17, 17, 17, 17, 8, 6, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 17, 39, 39, 39, 39, 39, 8, 8, 4, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/31 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1) `ZINC001567497627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567497627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001567497627 none CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 39, 39, 39, 39, 39, 8, 8, 4, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567497627 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 Building ZINC001567497627 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567497627 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 30) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1) `ZINC001567497627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567497627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001567497627 none CCc1noc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 17, 17, 17, 17, 8, 6, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 17, 39, 39, 39, 39, 39, 8, 8, 4, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 31) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1) `ZINC001567497627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567497627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001567497627 none CCc1noc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 18, 39, 39, 39, 39, 39, 8, 8, 4, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567497627 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567497627 Building ZINC001567574267 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567574267 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/32 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001567574267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567574267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567574267 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 24, 24, 19, 19, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 4, 7, 7, 7, 7, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/33 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001567574267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567574267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567574267 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 23, 23, 10, 19, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 4, 7, 7, 7, 7, 10, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567574267 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 Building ZINC001567574267 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567574267 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 32) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001567574267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567574267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567574267 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 24, 24, 19, 19, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 4, 7, 7, 7, 7, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 33) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1) `ZINC001567574267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567574267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567574267 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 23, 23, 10, 19, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 4, 7, 7, 7, 7, 10, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567574267 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567574267 Building ZINC001567777079 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567777079 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/34 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001567777079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567777079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567777079 none O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 14, 37, 50, 50, 38, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/35 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001567777079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567777079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567777079 none O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 15, 37, 50, 50, 49, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567777079 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 Building ZINC001567777079 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567777079 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 34) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001567777079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567777079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567777079 none O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 14, 37, 50, 50, 38, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 35) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001567777079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567777079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567777079 none O=C(N1CCC(COc2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 15, 37, 50, 50, 49, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001567777079 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001567777079 Building ZINC001568234661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568234661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/36 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1) `ZINC001568234661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568234661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568234661 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 22, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 2, 4, 4, 2, 5, 14, 14, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 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/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/37 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1) `ZINC001568234661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568234661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568234661 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 15, 23, 30, 30, 30, 30, 30, 30, 3, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 2, 3, 3, 2, 6, 15, 15, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 6, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001568234661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 Building ZINC001568234661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568234661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 36) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1) `ZINC001568234661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568234661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568234661 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 22, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 2, 4, 4, 2, 5, 14, 14, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 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/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 37) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1) `ZINC001568234661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568234661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001568234661 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 15, 23, 30, 30, 30, 30, 30, 30, 3, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 2, 3, 3, 2, 6, 15, 15, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 6, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001568234661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001568234661 Building ZINC001569703351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569703351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/38 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569703351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703351 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 9, 9, 9, 9, 9, 9, 16, 24, 24, 21, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 24, 24, 22, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/39 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569703351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703351 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 16, 25, 25, 16, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 25, 25, 23, 25, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569703351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 Building ZINC001569703351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569703351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 38) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569703351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703351 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 9, 9, 9, 9, 9, 9, 16, 24, 24, 21, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 24, 24, 22, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 39) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569703351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703351 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 16, 25, 25, 16, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 25, 25, 23, 25, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569703351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703351 Building ZINC001569703352 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569703352 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/40 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569703352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703352 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 16, 26, 26, 23, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 26, 26, 23, 26, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/41 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569703352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703352 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 9, 9, 9, 9, 9, 9, 16, 24, 24, 18, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 24, 24, 22, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569703352 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 Building ZINC001569703352 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569703352 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 40) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569703352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703352 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 16, 26, 26, 23, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 26, 26, 23, 26, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 41) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569703352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569703352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001569703352 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 9, 9, 9, 9, 9, 9, 16, 24, 24, 18, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 24, 24, 22, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569703352 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569703352 Building ZINC001569944157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/42 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944157 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 9, 10, 25, 25, 14, 20, 25, 25, 25, 25, 25, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 7, 7, 7] 48 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/43 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944157 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 15, 22, 25, 25, 25, 25, 25, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 Building ZINC001569944157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 42) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944157 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 9, 10, 25, 25, 14, 20, 25, 25, 25, 25, 25, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 7, 7, 7] 48 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 43) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944157 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 15, 22, 25, 25, 25, 25, 25, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944157 Building ZINC001569944158 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944158 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/44 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944158 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 21, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 5, 1, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 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]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/45 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944158 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 22, 24, 24, 24, 24, 24, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944158 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 Building ZINC001569944158 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944158 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 44) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944158 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 21, 25, 26, 26, 26, 26, 26, 13, 13, 13, 13, 5, 1, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 13, 13, 13, 13, 13, 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]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 45) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944158 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 17, 22, 24, 24, 24, 24, 24, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944158 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944158 Building ZINC001569944159 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944159 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/46 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944159 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 16, 23, 23, 23, 23, 23, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/47 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944159 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 23, 23, 13, 13, 23, 23, 23, 23, 23, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 23, 23, 23, 23, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944159 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 Building ZINC001569944159 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569944159 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 46) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569944159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944159 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 14, 16, 23, 23, 23, 23, 23, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 47) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001569944159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569944159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001569944159 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 10, 23, 23, 13, 13, 23, 23, 23, 23, 23, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 23, 23, 23, 23, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001569944159 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001569944159 Building ZINC001570637894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570637894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/48 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1) `ZINC001570637894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570637894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001570637894 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 10, 10, 9, 10, 33, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/49 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1) `ZINC001570637894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570637894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001570637894 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 9, 9, 8, 9, 32, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001570637894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 Building ZINC001570637894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001570637894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 48) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1) `ZINC001570637894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001570637894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001570637894 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 10, 10, 9, 10, 33, 50, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 49) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1) `ZINC001570637894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001570637894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001570637894 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 9, 9, 8, 9, 32, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001570637894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001570637894 Building ZINC001583033238 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583033238 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/50 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583033238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583033238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583033238 none O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 19, 30, 30, 19, 19, 30, 30, 30, 30, 30, 19, 1, 1, 1, 12, 12, 12, 12, 12, 6, 19, 30, 30, 30, 30, 19, 12, 12] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/51 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583033238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583033238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583033238 none O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 19, 29, 29, 19, 19, 29, 29, 29, 29, 29, 19, 1, 1, 1, 12, 12, 12, 12, 12, 6, 19, 29, 29, 29, 29, 19, 12, 12] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583033238 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 Building ZINC001583033238 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583033238 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 50) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583033238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583033238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583033238 none O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 19, 30, 30, 19, 19, 30, 30, 30, 30, 30, 19, 1, 1, 1, 12, 12, 12, 12, 12, 6, 19, 30, 30, 30, 30, 19, 12, 12] 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 51) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583033238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583033238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583033238 none O=C(Nc1cnn(c2ccc(C(F)(F)F)cc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 19, 29, 29, 19, 19, 29, 29, 29, 29, 29, 19, 1, 1, 1, 12, 12, 12, 12, 12, 6, 19, 29, 29, 29, 29, 19, 12, 12] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583033238 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583033238 Building ZINC001583071972 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583071972 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/52 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/53 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/54 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/54' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/55 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/55' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583071972 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 Building ZINC001583071972 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583071972 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 52) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 53) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 54) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 55) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583071972 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 Building ZINC001583071972 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583071972 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 52) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 53) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 54) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 55) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583071972 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 Building ZINC001583071972 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583071972 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 52) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 53) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 11, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 3, 3, 2, 5, 5, 6, 6, 6, 6, 11, 11, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 54) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 55) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl) `ZINC001583071972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583071972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583071972 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN(C)C2CCCCC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 14, 18, 18, 35, 35, 35, 35, 35, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 6, 6, 6, 14, 14, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583071972 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583071972 Building ZINC001583159087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583159087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/56 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583159087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 10, 10, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/57 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583159087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583159087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 Building ZINC001583159087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583159087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 56) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583159087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 10, 10, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 57) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583159087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583159087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159087 Building ZINC001583159088 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583159088 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/58 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583159088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159088 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/59 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583159088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159088 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 97 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583159088 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 Building ZINC001583159088 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583159088 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 58) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583159088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159088 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 59) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21) `ZINC001583159088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583159088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583159088 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCc2c3cc(Br)ccc3[nH]c21 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', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.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, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 10, 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]) total number of confs: 97 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583159088 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583159088 Building ZINC001583193214 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583193214 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/60 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/60' -> `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(Cl)cc(Br)c1) `ZINC001583193214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583193214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001583193214 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 16, 26, 26, 26, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 5, 26, 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]) total number of confs: 96 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/61 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/61' -> `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(Cl)cc(Br)c1) `ZINC001583193214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583193214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001583193214 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 8, 26, 26, 26, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 5, 26, 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]) total number of confs: 118 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583193214 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 Building ZINC001583193214 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583193214 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 60) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1) `ZINC001583193214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583193214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001583193214 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 16, 26, 26, 26, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 5, 26, 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]) total number of confs: 96 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 61) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1) `ZINC001583193214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583193214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001583193214 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 8, 26, 26, 26, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 5, 26, 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]) total number of confs: 118 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583193214 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583193214 Building ZINC001583207399 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583207399 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/62 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1) `ZINC001583207399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583207399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583207399 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 40, 40, 32, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 40, 40, 40, 40, 40, 40, 40, 11, 11, 2, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/63 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1) `ZINC001583207399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583207399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583207399 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 40, 40, 32, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 40, 40, 40, 40, 40, 40, 40, 11, 11, 2, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583207399 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 Building ZINC001583207399 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583207399 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 62) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1) `ZINC001583207399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583207399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583207399 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 40, 40, 32, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 40, 40, 40, 40, 40, 40, 40, 11, 11, 2, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 63) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1) `ZINC001583207399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583207399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583207399 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 40, 40, 32, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 40, 40, 40, 40, 40, 40, 40, 11, 11, 2, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583207399 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583207399 Building ZINC001583224537 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583224537 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/64 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Br)s4)CC3)c2c1) `ZINC001583224537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583224537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583224537 none COc1ccc2[nH]cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Br)s4)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 31, 31, 36, 36, 36, 31, 31, 31, 8, 8, 8, 8, 8, 4, 4, 8, 8, 8, 8, 31] 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]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/65 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Br)s4)CC3)c2c1) `ZINC001583224537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583224537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583224537 none COc1ccc2[nH]cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Br)s4)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 38, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 38, 38, 39, 39, 39, 38, 38, 38, 12, 12, 12, 12, 12, 3, 3, 12, 12, 12, 12, 38] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583224537 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 Building ZINC001583224537 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583224537 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 64) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Br)s4)CC3)c2c1) `ZINC001583224537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583224537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583224537 none COc1ccc2[nH]cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Br)s4)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 31, 31, 36, 36, 36, 31, 31, 31, 8, 8, 8, 8, 8, 4, 4, 8, 8, 8, 8, 31] 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]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 65) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Br)s4)CC3)c2c1) `ZINC001583224537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583224537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583224537 none COc1ccc2[nH]cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Br)s4)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 38, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 38, 38, 39, 39, 39, 38, 38, 38, 12, 12, 12, 12, 12, 3, 3, 12, 12, 12, 12, 38] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583224537 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583224537 Building ZINC001583234966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583234966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/66 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583234966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583234966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001583234966 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 13, 24, 24, 24, 24, 45, 45, 37, 37, 45, 45, 45, 45, 45, 24, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 45, 45, 45, 45, 24, 24, 24, 24, 3, 1, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/67 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583234966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583234966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001583234966 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 23, 23, 23, 23, 46, 46, 38, 38, 46, 46, 46, 46, 46, 23, 23, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 46, 46, 46, 46, 23, 23, 23, 23, 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]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583234966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 Building ZINC001583234966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583234966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 66) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583234966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583234966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001583234966 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 13, 24, 24, 24, 24, 45, 45, 37, 37, 45, 45, 45, 45, 45, 24, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 45, 45, 45, 45, 24, 24, 24, 24, 3, 1, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 67) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583234966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583234966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001583234966 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 23, 23, 23, 23, 46, 46, 38, 38, 46, 46, 46, 46, 46, 23, 23, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 46, 46, 46, 46, 23, 23, 23, 23, 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]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583234966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583234966 Building ZINC001583273178 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583273178 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/68 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC) `ZINC001583273178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583273178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583273178 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 24, 30, 30, 30, 30, 30, 6, 3, 4, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/69 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC) `ZINC001583273178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583273178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583273178 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 23, 28, 28, 28, 28, 28, 6, 3, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583273178 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 Building ZINC001583273178 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583273178 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 68) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC) `ZINC001583273178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583273178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583273178 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 24, 30, 30, 30, 30, 30, 6, 3, 4, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 69) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC) `ZINC001583273178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583273178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583273178 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 22, 23, 28, 28, 28, 28, 28, 6, 3, 4, 4, 4, 4, 6, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583273178 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583273178 Building ZINC001583349142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583349142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/70 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSCc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583349142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583349142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583349142 none O=C(NCCSCc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 6, 15, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 3, 5, 5, 6, 6, 30, 30, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/71 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSCc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583349142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583349142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583349142 none O=C(NCCSCc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 6, 15, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 3, 5, 5, 6, 6, 30, 30, 40, 40, 40, 40, 40, 40, 40, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583349142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 Building ZINC001583349142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583349142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 70) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCCSCc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583349142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583349142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583349142 none O=C(NCCSCc1cccc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 6, 15, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 3, 5, 5, 6, 6, 30, 30, 40, 40, 40, 40, 40, 40, 40, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 71) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCCSCc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583349142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583349142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583349142 none O=C(NCCSCc1cccc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 6, 15, 30, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 3, 5, 5, 6, 6, 30, 30, 40, 40, 40, 40, 40, 40, 40, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583349142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583349142 Building ZINC001583350087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583350087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/72 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/72' -> `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)NCCSCc1cccc2ccccc21) `ZINC001583350087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583350087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001583350087 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21 NO_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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 17, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 7, 7, 8, 8, 29, 29, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/73 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/73' -> `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)NCCSCc1cccc2ccccc21) `ZINC001583350087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583350087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001583350087 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21 NO_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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 15, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 7, 29, 29, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583350087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 Building ZINC001583350087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583350087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 72) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21) `ZINC001583350087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583350087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001583350087 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21 NO_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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 17, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 7, 7, 8, 8, 29, 29, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 73) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21) `ZINC001583350087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583350087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001583350087 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCSCc1cccc2ccccc21 NO_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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 15, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 7, 29, 29, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583350087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583350087 Building ZINC001583370566 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583370566 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/74 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001583370566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583370566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001583370566 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 25, 25, 35, 35, 35, 35, 12, 12, 8, 3, 9, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 4, 4] 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/75 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001583370566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583370566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001583370566 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 25, 25, 37, 37, 37, 37, 14, 14, 10, 3, 11, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583370566 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 Building ZINC001583370566 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583370566 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 74) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001583370566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583370566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001583370566 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 25, 25, 35, 35, 35, 35, 12, 12, 8, 3, 9, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 4, 4] 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: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 75) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001583370566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583370566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001583370566 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 25, 25, 37, 37, 37, 37, 14, 14, 10, 3, 11, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583370566 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583370566 Building ZINC001583390849 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583390849 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/76 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC001583390849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583390849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001583390849 none Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 15, 15, 23, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 73 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/77 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC001583390849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583390849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001583390849 none Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 14, 14, 23, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583390849 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 Building ZINC001583390849 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583390849 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 76) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC001583390849.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583390849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001583390849 none Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 15, 15, 23, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 73 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 77) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2) `ZINC001583390849.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583390849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001583390849 none Cc1ccc(NC(=O)OC(C)(C)C)c2c1N(C(=O)[C@]([O-])([SiH3])c1ccc3c(c1)CCC3)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 14, 14, 23, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583390849 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583390849 Building ZINC001583452885 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583452885 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/78 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583452885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583452885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583452885 none Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 15 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]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/79 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583452885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583452885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583452885 none Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 15 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]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583452885 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 Building ZINC001583452885 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583452885 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 78) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583452885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583452885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583452885 none Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 15 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]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 79) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583452885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583452885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583452885 none Cc1cc(Br)c2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 15 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]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583452885 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583452885 Building ZINC001583461211 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461211 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/80 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/81 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/82 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/82' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/83 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/83' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461211 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 Building ZINC001583461211 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461211 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 80) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 81) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 82) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 83) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461211 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 Building ZINC001583461211 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461211 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 80) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 81) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 82) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 83) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461211 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 Building ZINC001583461211 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461211 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 80) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 81) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 82) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 4, 7, 22, 31, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 10, 10, 2, 2, 2, 2, 2, 2, 4, 10, 10, 22, 22, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 83) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)cc1) `ZINC001583461211.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461211 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 6, 8, 21, 30, 40, 50, 50, 50, 50, 50, 50, 30, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2, 3, 9, 9, 21, 21, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461211 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461211 Building ZINC001583461212 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461212 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/84 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/85 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/86 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/86' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/87 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/87' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461212 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 Building ZINC001583461212 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461212 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 84) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 85) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 86) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 87) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461212 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 Building ZINC001583461212 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461212 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 84) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 85) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 86) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 87) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461212 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 Building ZINC001583461212 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583461212 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 84) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 85) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 86) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 30, 30, 42, 50, 50, 50, 50, 50, 50, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 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, 61]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 87) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)cc1) `ZINC001583461212.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583461212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583461212 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(CN(C[C@@H]2CCCCO2)C(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 10, 5, 5, 7, 5, 5, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 3, 29, 31, 43, 50, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 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, 61]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583461212 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583461212 Building ZINC001583522106 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583522106 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/88 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001583522106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583522106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001583522106 none Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 10, 16, 16, 16, 50, 50, 18, 50, 50, 50, 50, 50, 50, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 16, 50, 50, 31, 50, 10, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/89 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001583522106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583522106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001583522106 none Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 1 hydrogens 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, 9, 9, 9, 9, 9, 15, 15, 15, 50, 50, 15, 50, 50, 50, 50, 50, 50, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 15, 50, 50, 25, 50, 9, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583522106 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 Building ZINC001583522106 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583522106 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 88) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001583522106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583522106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001583522106 none Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 1 hydrogens 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, 10, 10, 10, 10, 10, 16, 16, 16, 50, 50, 18, 50, 50, 50, 50, 50, 50, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 10, 10, 16, 50, 50, 31, 50, 10, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 89) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001583522106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583522106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001583522106 none Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 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] 1 hydrogens 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, 9, 9, 9, 9, 9, 15, 15, 15, 50, 50, 15, 50, 50, 50, 50, 50, 50, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 9, 9, 9, 15, 50, 50, 25, 50, 9, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583522106 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583522106 Building ZINC001583552248 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583552248 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/90 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/90' -> `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)Nc1cccc(N(C)C)c1C) `ZINC001583552248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583552248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583552248 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/91 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/91' -> `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)Nc1cccc(N(C)C)c1C) `ZINC001583552248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583552248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583552248 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583552248 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 Building ZINC001583552248 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583552248 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 90) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C) `ZINC001583552248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583552248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583552248 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 91) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C) `ZINC001583552248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583552248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583552248 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(N(C)C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583552248 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583552248 Building ZINC001583580351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583580351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/92 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)c2)cn1) `ZINC001583580351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583580351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583580351 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 13, 24, 24, 23, 24, 24, 24, 24, 25, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 13, 13, 24, 24, 24, 31, 31, 31, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/93 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)c2)cn1) `ZINC001583580351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583580351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583580351 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 12, 23, 23, 22, 23, 23, 23, 23, 24, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 23, 23, 23, 30, 30, 30, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583580351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 Building ZINC001583580351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583580351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 92) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)c2)cn1) `ZINC001583580351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583580351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583580351 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 13, 24, 24, 23, 24, 24, 24, 24, 25, 31, 31, 31, 31, 31, 31, 31, 5, 5, 10, 10, 10, 10, 10, 5, 2, 13, 13, 24, 24, 24, 31, 31, 31, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 93) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)c2)cn1) `ZINC001583580351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583580351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001583580351 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(Cl)cc2Oc2ccc(F)c(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', '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, 16, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 12, 23, 23, 22, 23, 23, 23, 23, 24, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 23, 23, 23, 30, 30, 30, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583580351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583580351 Building ZINC001583588938 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583588938 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/94 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583588938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583588938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001583588938 none O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 32, 32, 32, 32, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/95 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583588938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583588938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001583588938 none O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 31, 31, 31, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 31, 31, 31, 31, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583588938 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 Building ZINC001583588938 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583588938 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 94) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583588938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583588938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001583588938 none O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 32, 32, 32, 32, 32, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 32, 32, 32, 32, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 95) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001583588938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583588938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001583588938 none O=C(Nc1ccc2nc(c3ccccn3)oc2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 31, 31, 31, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 4, 16, 16, 31, 31, 31, 31, 16, 9, 9] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583588938 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583588938 Building ZINC001583592946 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583592946 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/96 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)CC2)cc1Cl) `ZINC001583592946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583592946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583592946 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)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', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 4, 17, 17, 17, 4, 4, 6, 6, 6, 15, 15, 15, 6, 6, 4, 17, 7, 17, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/97 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)CC2)cc1Cl) `ZINC001583592946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583592946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583592946 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)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', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 4, 13, 13, 13, 4, 4, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 7, 13, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583592946 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 Building ZINC001583592946 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583592946 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 96) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)CC2)cc1Cl) `ZINC001583592946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583592946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583592946 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)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', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 4, 17, 17, 17, 4, 4, 6, 6, 6, 15, 15, 15, 6, 6, 4, 17, 7, 17, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 97) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)CC2)cc1Cl) `ZINC001583592946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583592946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583592946 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2(c3cc(Cl)cc(Br)c3)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', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 4, 13, 13, 13, 4, 4, 6, 6, 6, 12, 12, 12, 6, 6, 4, 13, 7, 13, 4, 4, 4, 4, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583592946 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583592946 Building ZINC001583604817 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583604817 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/98 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583604817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604817 none O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 8, 8, 8, 8, 8, 8, 37, 37, 37, 46, 46, 37, 46, 46, 37, 37, 37, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 37, 46, 46, 37, 46, 46, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/99 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583604817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604817 none O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 7, 7, 7, 7, 7, 7, 28, 28, 28, 44, 44, 39, 44, 44, 28, 28, 28, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 28, 44, 44, 41, 44, 44, 7, 7, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583604817 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 Building ZINC001583604817 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583604817 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 98) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583604817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604817 none O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 8, 8, 8, 8, 8, 8, 37, 37, 37, 46, 46, 37, 46, 46, 37, 37, 37, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 37, 46, 46, 37, 46, 46, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 99) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583604817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604817 none O=C(N1CCC[C@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 7, 7, 7, 7, 7, 7, 28, 28, 28, 44, 44, 39, 44, 44, 28, 28, 28, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 28, 44, 44, 41, 44, 44, 7, 7, 3, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583604817 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604817 Building ZINC001583604824 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583604824 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/100 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583604824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604824 none O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 5, 7, 7, 7, 7, 7, 7, 29, 29, 29, 44, 44, 29, 44, 44, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 29, 44, 44, 29, 44, 44, 7, 7, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/101 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583604824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604824 none O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 8, 8, 8, 8, 8, 8, 38, 38, 38, 46, 46, 45, 46, 46, 38, 38, 38, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 38, 46, 46, 45, 46, 46, 8, 8, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583604824 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 Building ZINC001583604824 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583604824 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 100) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583604824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604824 none O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 5, 7, 7, 7, 7, 7, 7, 29, 29, 29, 44, 44, 29, 44, 44, 29, 29, 29, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 29, 44, 44, 29, 44, 44, 7, 7, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 101) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583604824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583604824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001583604824 none O=C(N1CCC[C@@H](c2cc(c3ccccc3)[nH]n2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 8, 8, 8, 8, 8, 8, 38, 38, 38, 46, 46, 45, 46, 46, 38, 38, 38, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 38, 46, 46, 45, 46, 46, 8, 8, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583604824 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583604824 Building ZINC001583701054 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583701054 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/102 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001583701054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583701054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001583701054 none CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 2, 5, 14, 22, 22, 22, 20, 22, 22, 22, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 22, 22, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/103 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001583701054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583701054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001583701054 none CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 2, 5, 14, 22, 22, 22, 18, 22, 22, 22, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 22, 22, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583701054 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 Building ZINC001583701054 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583701054 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 102) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001583701054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583701054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001583701054 none CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 2, 5, 14, 22, 22, 22, 20, 22, 22, 22, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 22, 22, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 103) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001583701054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583701054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001583701054 none CC(C)N(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 2, 5, 14, 22, 22, 22, 18, 22, 22, 22, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 14, 14, 22, 22, 22, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583701054 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583701054 Building ZINC001583750085 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583750085 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/104 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/104' -> `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)Nc1cc2c(cn1)CCCC2) `ZINC001583750085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583750085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583750085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/105 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/105' -> `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)Nc1cc2c(cn1)CCCC2) `ZINC001583750085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583750085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583750085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583750085 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 Building ZINC001583750085 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583750085 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 104) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2) `ZINC001583750085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583750085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583750085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 105) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2) `ZINC001583750085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583750085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583750085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cn1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583750085 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583750085 Building ZINC001583778926 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583778926 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/106 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc21) `ZINC001583778926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583778926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001583778926 none CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 3, 3, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/107 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc21) `ZINC001583778926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583778926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001583778926 none CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 3, 3, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583778926 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 Building ZINC001583778926 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583778926 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 106) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc21) `ZINC001583778926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583778926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001583778926 none CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 3, 3, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 107) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc21) `ZINC001583778926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583778926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001583778926 none CC(C)(C)OC(=O)N1CCCc2cc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 3, 3, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583778926 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583778926 Building ZINC001583832416 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583832416 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/108 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583832416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832416 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 18, 29, 29, 18, 29, 29, 29, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 29, 29, 26, 29, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/109 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583832416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832416 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 25, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 28, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583832416 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 Building ZINC001583832416 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583832416 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 108) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583832416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832416 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 18, 29, 29, 18, 29, 29, 29, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 29, 29, 26, 29, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 109) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583832416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832416 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 25, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 28, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583832416 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832416 Building ZINC001583832417 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583832417 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/110 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583832417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832417 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 19, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 25, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/111 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583832417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832417 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 9, 9, 9, 9, 9, 9, 18, 28, 28, 18, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 28, 28, 24, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583832417 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 Building ZINC001583832417 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583832417 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 110) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583832417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832417 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 9, 9, 9, 9, 9, 9, 9, 19, 30, 30, 19, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 30, 30, 25, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 111) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001583832417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583832417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001583832417 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 9, 9, 9, 9, 9, 9, 9, 18, 28, 28, 18, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 28, 28, 24, 28, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583832417 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583832417 Building ZINC001583891171 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583891171 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/112 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)cc3)CC2)cc1Cl) `ZINC001583891171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583891171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583891171 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 3, 4, 28, 29, 29, 29, 6, 6, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/113 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)cc3)CC2)cc1Cl) `ZINC001583891171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583891171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583891171 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 2, 4, 25, 25, 25, 25, 6, 6, 2, 2, 3, 3, 3, 6, 6, 6, 3, 3, 2, 2, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 2, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583891171 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 Building ZINC001583891171 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583891171 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 112) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)cc3)CC2)cc1Cl) `ZINC001583891171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583891171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583891171 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 3, 4, 28, 29, 29, 29, 6, 6, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 113) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)cc3)CC2)cc1Cl) `ZINC001583891171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583891171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001583891171 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(OC(F)(F)F)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 2, 4, 25, 25, 25, 25, 6, 6, 2, 2, 3, 3, 3, 6, 6, 6, 3, 3, 2, 2, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 2, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583891171 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583891171 Building ZINC001583899745 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899745 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/114 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/115 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/116 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/116' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/117 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/117' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899745 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 Building ZINC001583899745 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899745 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 114) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 115) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 116) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 117) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899745 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 Building ZINC001583899745 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899745 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 114) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 115) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 116) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 117) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899745 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 Building ZINC001583899745 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899745 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 114) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 115) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 31, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 31, 31, 31, 14, 14, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 116) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 117) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899745 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 20, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 1, 3, 46, 46, 46] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899745 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899745 Building ZINC001583899746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/118 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/119 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/120 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/120' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/121 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/121' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 Building ZINC001583899746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 118) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 119) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 120) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 121) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 Building ZINC001583899746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 118) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 119) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 120) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 121) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 Building ZINC001583899746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 118) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 119) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 13, 13, 2, 3, 1, 3, 48, 48, 48] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 120) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 121) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001583899746.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899746 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 32, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899746 Building ZINC001583899747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/122 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/123 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/124 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/125 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 Building ZINC001583899747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 122) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 123) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 124) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 125) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 Building ZINC001583899747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 122) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 123) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 124) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 125) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 Building ZINC001583899747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 122) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 123) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 26, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 26, 26, 49, 49, 49, 49, 49, 49, 49, 26, 26, 26, 26, 26, 26, 26, 11, 11, 2, 3, 1, 3, 49, 49, 49] 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 124) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 125) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899747.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899747 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 13, 13, 2, 3, 1, 3, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899747 Building ZINC001583899748 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899748 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/126 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/127 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/128 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/128' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/129 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/129' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899748 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 Building ZINC001583899748 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899748 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 126) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 127) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 128) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 129) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899748 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 Building ZINC001583899748 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899748 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 126) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 127) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 128) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 129) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899748 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 Building ZINC001583899748 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001583899748 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 126) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 127) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 27, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 27, 27, 14, 14, 3, 3, 3, 3, 46, 46, 46] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 128) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 129) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001583899748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001583899748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001583899748 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1c1ccc(Cl)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 30, 30, 30, 30, 30, 30, 14, 14, 3, 3, 1, 3, 47, 47, 47] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583899748 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583899748 Building ZINC001583968220 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583968220 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/130 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583968220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583968220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001583968220 none O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 12, 21, 21, 21, 21, 44, 44, 21, 28, 44, 44, 44, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 44, 44, 44, 21, 21, 21, 21, 3, 1, 3] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/131 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583968220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583968220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001583968220 none O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 21, 21, 21, 21, 46, 46, 21, 31, 46, 46, 46, 21, 21, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 46, 46, 46, 21, 21, 21, 21, 3, 3, 3] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583968220 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 Building ZINC001583968220 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583968220 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 130) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583968220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583968220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001583968220 none O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 12, 21, 21, 21, 21, 44, 44, 21, 28, 44, 44, 44, 21, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 44, 44, 44, 21, 21, 21, 21, 3, 1, 3] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 131) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583968220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583968220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001583968220 none O=C(N1CCN(c2ccc(Cl)cc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 21, 21, 21, 21, 46, 46, 21, 31, 46, 46, 46, 21, 21, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 46, 46, 46, 21, 21, 21, 21, 3, 3, 3] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583968220 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583968220 Building ZINC001583991670 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583991670 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/132 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br) `ZINC001583991670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583991670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583991670 none Cc1cc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 1, 1, 17, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 22, 22, 16, 22, 22, 22, 22, 22, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/133 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br) `ZINC001583991670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583991670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583991670 none Cc1cc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 1, 1, 17, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 7, 7, 7, 7, 7, 19, 19, 14, 19, 19, 19, 19, 19, 3, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583991670 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 Building ZINC001583991670 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583991670 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 132) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br) `ZINC001583991670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583991670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583991670 none Cc1cc(C2(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 1, 1, 17, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 22, 22, 16, 22, 22, 22, 22, 22, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 133) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br) `ZINC001583991670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583991670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001583991670 none Cc1cc(C2(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CCCCC2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 1, 1, 1, 17, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 8, 7, 7, 7, 7, 7, 19, 19, 14, 19, 19, 19, 19, 19, 3, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583991670 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583991670 Building ZINC001583995951 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583995951 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/134 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583995951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583995951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583995951 none O=C(N1CCc2c(F)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 47 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/135 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(F)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583995951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583995951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583995951 none O=C(N1CCc2c(F)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 46 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583995951 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 Building ZINC001583995951 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583995951 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 134) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2c(F)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583995951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583995951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583995951 none O=C(N1CCc2c(F)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 47 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 135) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2c(F)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001583995951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583995951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001583995951 none O=C(N1CCc2c(F)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 15, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 46 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001583995951 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001583995951 Building ZINC001584004744 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584004744 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/136 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584004744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584004744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584004744 none O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/137 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584004744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584004744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584004744 none O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584004744 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 Building ZINC001584004744 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584004744 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 136) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584004744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584004744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584004744 none O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 137) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584004744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584004744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584004744 none O=C(N1CCc2ccc(c3ccccc3)cc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 17, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 17, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584004744 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584004744 Building ZINC001584084964 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584084964 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/138 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584084964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084964 none CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 17, 17, 12, 17, 17, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 17, 17, 12, 17, 6, 12, 17, 17, 17, 17, 17, 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]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/139 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584084964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084964 none CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 6, 9, 9, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 18, 18, 18, 18, 6, 12, 18, 18, 12, 18, 18, 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]) total number of confs: 113 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584084964 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 Building ZINC001584084964 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584084964 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 138) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584084964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084964 none CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 17, 17, 12, 17, 17, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 17, 17, 12, 17, 6, 12, 17, 17, 17, 17, 17, 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]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 139) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584084964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084964 none CC(C)(C)[C@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 6, 9, 9, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 18, 18, 18, 18, 6, 12, 18, 18, 12, 18, 18, 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]) total number of confs: 113 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584084964 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084964 Building ZINC001584084965 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584084965 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/140 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584084965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084965 none CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 6, 8, 8, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 17, 17, 17, 17, 6, 12, 18, 18, 12, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/141 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584084965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084965 none CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 6, 9, 9, 11, 16, 16, 14, 16, 16, 16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 17, 17, 12, 17, 17, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 14, 16, 6, 12, 17, 17, 12, 17, 17, 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]) total number of confs: 103 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584084965 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 Building ZINC001584084965 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584084965 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 140) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584084965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084965 none CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 6, 8, 8, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 18, 18, 12, 18, 18, 12, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 17, 17, 17, 17, 6, 12, 18, 18, 12, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 141) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001584084965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584084965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584084965 none CC(C)(C)[C@@H](Cc1ccccc1C(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 11, 6, 9, 9, 11, 16, 16, 14, 16, 16, 16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 17, 17, 12, 17, 17, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 14, 16, 6, 12, 17, 17, 12, 17, 17, 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]) total number of confs: 103 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584084965 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584084965 Building ZINC001584105864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584105864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/142 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/142' -> `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)Nc1cccc(Cl)c1OCC(F)F) `ZINC001584105864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584105864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001584105864 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 13, 30, 37, 37, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 4, 9, 9, 9, 30, 30, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/143 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/143' -> `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)Nc1cccc(Cl)c1OCC(F)F) `ZINC001584105864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584105864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001584105864 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 14, 31, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 10, 10, 10, 31, 31, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584105864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 Building ZINC001584105864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584105864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 142) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F) `ZINC001584105864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584105864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001584105864 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 13, 30, 37, 37, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 4, 9, 9, 9, 30, 30, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 143) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F) `ZINC001584105864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584105864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001584105864 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 14, 31, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 10, 10, 10, 31, 31, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584105864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584105864 Building ZINC001584147564 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584147564 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/144 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1) `ZINC001584147564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584147564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001584147564 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 23, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 24, 46, 46, 46, 6, 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]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/145 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1) `ZINC001584147564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584147564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001584147564 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 11, 47, 47, 47, 19, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 11, 47, 22, 47, 47, 47, 6, 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]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584147564 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 Building ZINC001584147564 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584147564 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 144) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1) `ZINC001584147564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584147564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001584147564 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 11, 46, 46, 46, 23, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 11, 46, 24, 46, 46, 46, 6, 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]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 145) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1) `ZINC001584147564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584147564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001584147564 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(I)cc(C(F)(F)F)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 11, 11, 11, 47, 47, 47, 19, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 11, 47, 22, 47, 47, 47, 6, 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]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584147564 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584147564 Building ZINC001584154142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584154142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/146 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C) `ZINC001584154142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584154142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584154142 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 7, 10, 10, 7, 10, 10, 10, 10, 32, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 7, 10, 10, 10, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/147 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C) `ZINC001584154142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584154142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584154142 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 8, 11, 11, 8, 11, 11, 11, 11, 31, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 8, 11, 11, 11, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584154142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 Building ZINC001584154142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584154142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 146) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C) `ZINC001584154142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584154142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584154142 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 7, 10, 10, 7, 10, 10, 10, 10, 32, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 7, 10, 10, 10, 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 147) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C) `ZINC001584154142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584154142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584154142 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Cl)cc1Oc1ccc(C)cc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 8, 11, 11, 8, 11, 11, 11, 11, 31, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 8, 11, 11, 11, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584154142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584154142 Building ZINC001584159768 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584159768 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/148 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl) `ZINC001584159768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584159768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584159768 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 2, 9, 9, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 15, 15, 15, 9, 9, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 66 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/149 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl) `ZINC001584159768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584159768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584159768 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 16, 16, 16, 10, 10, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584159768 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 Building ZINC001584159768 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584159768 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 148) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl) `ZINC001584159768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584159768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584159768 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 2, 9, 9, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 15, 15, 15, 9, 9, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 66 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 149) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl) `ZINC001584159768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584159768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584159768 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccccc2)CCC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 16, 16, 16, 10, 10, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584159768 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584159768 Building ZINC001584162977 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584162977 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/150 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584162977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584162977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584162977 none O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 17, 28, 28, 25, 28, 28, 28, 28, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 10, 5, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/151 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584162977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584162977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584162977 none O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 18, 28, 28, 25, 28, 28, 28, 28, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 6, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584162977 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 Building ZINC001584162977 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584162977 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 150) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584162977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584162977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584162977 none O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 17, 28, 28, 25, 28, 28, 28, 28, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 10, 5, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 151) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584162977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584162977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584162977 none O=C(NC1(c2ccc(F)cc2F)CCCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 18, 28, 28, 25, 28, 28, 28, 28, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 6, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584162977 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584162977 Building ZINC001584186584 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584186584 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/152 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21) `ZINC001584186584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584186584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584186584 none CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 37, 44, 37, 37, 37, 37, 37, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 13, 13, 3, 2, 2, 2, 2, 37, 37, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/153 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21) `ZINC001584186584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584186584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584186584 none CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 40, 45, 40, 40, 40, 40, 40, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 3, 2, 2, 2, 2, 40, 40, 40] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584186584 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 Building ZINC001584186584 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584186584 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 152) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21) `ZINC001584186584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584186584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584186584 none CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 37, 44, 37, 37, 37, 37, 37, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 13, 13, 3, 2, 2, 2, 2, 37, 37, 37] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 153) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21) `ZINC001584186584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584186584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584186584 none CC(C)(C)OC(=O)N1CCCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 40, 45, 40, 40, 40, 40, 40, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 11, 11, 3, 2, 2, 2, 2, 40, 40, 40] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584186584 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584186584 Building ZINC001584229288 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584229288 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/154 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)n1) `ZINC001584229288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584229288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584229288 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 22, 22, 14, 22, 22, 22, 22, 22, 21, 14, 14, 14, 14, 14, 8, 7, 7, 7, 7, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/155 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)n1) `ZINC001584229288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584229288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584229288 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 21, 21, 20, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584229288 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 Building ZINC001584229288 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584229288 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 154) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)n1) `ZINC001584229288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584229288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584229288 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 22, 22, 14, 22, 22, 22, 22, 22, 21, 14, 14, 14, 14, 14, 8, 7, 7, 7, 7, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 155) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)n1) `ZINC001584229288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584229288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584229288 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(C(F)(F)F)c2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 21, 21, 20, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584229288 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584229288 Building ZINC001584236427 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584236427 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/156 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1) `ZINC001584236427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584236427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584236427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/157 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1) `ZINC001584236427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584236427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584236427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 10, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584236427 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 Building ZINC001584236427 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584236427 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 156) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1) `ZINC001584236427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584236427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584236427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 10, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 157) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1) `ZINC001584236427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584236427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584236427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCC[C@H](C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 10, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584236427 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584236427 Building ZINC001584238954 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584238954 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/158 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584238954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238954 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 20, 25, 11, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 11, 11, 3, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/159 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584238954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238954 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 23, 27, 13, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 13, 13, 4, 3, 3, 3, 3, 15, 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, 55, 56]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584238954 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 Building ZINC001584238954 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584238954 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 158) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584238954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238954 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 20, 25, 11, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 11, 11, 3, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 159) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584238954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238954 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 23, 27, 13, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 13, 13, 4, 3, 3, 3, 3, 15, 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, 55, 56]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584238954 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238954 Building ZINC001584238955 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584238955 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/160 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584238955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238955 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 26, 13, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 13, 13, 4, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/161 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584238955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238955 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 20, 26, 11, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 11, 11, 3, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584238955 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 Building ZINC001584238955 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584238955 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 160) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584238955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238955 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 22, 26, 13, 6, 4, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 13, 13, 4, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 161) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1) `ZINC001584238955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584238955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584238955 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2ccccc2c1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 20, 26, 11, 4, 3, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 11, 11, 3, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584238955 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584238955 Building ZINC001584239753 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584239753 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/162 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584239753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239753 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 17, 24, 24, 28, 28, 28, 28, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 10, 3, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/163 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584239753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239753 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 20, 27, 27, 29, 29, 29, 29, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584239753 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 Building ZINC001584239753 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584239753 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 162) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584239753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239753 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 17, 24, 24, 28, 28, 28, 28, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 10, 10, 3, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 163) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584239753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239753 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 20, 27, 27, 29, 29, 29, 29, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584239753 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239753 Building ZINC001584239754 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584239754 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/164 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584239754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239754 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 17, 23, 23, 27, 27, 27, 27, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/165 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584239754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239754 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 16, 23, 23, 27, 27, 27, 27, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 3, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584239754 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 Building ZINC001584239754 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584239754 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 164) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584239754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239754 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 17, 23, 23, 27, 27, 27, 27, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 165) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1) `ZINC001584239754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584239754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584239754 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)OC(C)(C)C)c2ccc3ccccc3c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 16, 23, 23, 27, 27, 27, 27, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 10, 3, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584239754 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584239754 Building ZINC001584264161 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584264161 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/166 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/166' -> `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(C(C)C)nn1c1ccccc1) `ZINC001584264161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584264161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584264161 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 37, 37, 19, 19, 19, 21, 21, 21, 21, 21, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 19, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/167 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/167' -> `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(C(C)C)nn1c1ccccc1) `ZINC001584264161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584264161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584264161 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 37, 37, 19, 19, 19, 21, 21, 21, 21, 21, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 19, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584264161 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 Building ZINC001584264161 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584264161 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 166) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1) `ZINC001584264161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584264161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584264161 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 37, 37, 19, 19, 19, 21, 21, 21, 21, 21, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 19, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 165 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 167) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1) `ZINC001584264161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584264161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001584264161 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C(C)C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 1, 5, 5, 9, 19, 19, 19, 37, 37, 19, 19, 19, 21, 21, 21, 21, 21, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 19, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584264161 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584264161 Building ZINC001584270280 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584270280 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/168 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)C1) `ZINC001584270280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584270280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270280 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 5, 10, 10, 10, 10, 4, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 83 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/169 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)C1) `ZINC001584270280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584270280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270280 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 5, 9, 9, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 55, 56]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584270280 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 Building ZINC001584270280 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584270280 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 168) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)C1) `ZINC001584270280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584270280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270280 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 5, 10, 10, 10, 10, 4, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 83 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 169) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)C1) `ZINC001584270280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584270280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270280 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 5, 9, 9, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 55, 56]) total number of confs: 68 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584270280 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270280 Building ZINC001584270281 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584270281 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/170 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)C1) `ZINC001584270281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584270281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270281 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 6, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 5, 9, 9, 9, 9, 4, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 55, 56]) total number of confs: 79 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/171 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)C1) `ZINC001584270281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584270281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270281 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 5, 10, 10, 10, 10, 4, 3, 3, 3, 21, 21, 21, 21, 3, 3, 3, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584270281 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 Building ZINC001584270281 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584270281 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 170) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)C1) `ZINC001584270281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584270281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270281 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 6, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 5, 9, 9, 9, 9, 4, 3, 3, 3, 22, 22, 10, 22, 3, 3, 3, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 55, 56]) total number of confs: 79 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 171) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)C1) `ZINC001584270281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584270281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584270281 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C2CCCC2)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 5, 10, 10, 10, 10, 4, 3, 3, 3, 21, 21, 21, 21, 3, 3, 3, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584270281 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584270281 Building ZINC001584271978 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584271978 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/172 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl) `ZINC001584271978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584271978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584271978 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 5, 5, 5, 14, 14, 5, 9, 14, 14, 14, 14, 14, 14, 10, 10, 10, 19, 19, 19, 10, 10, 5, 14, 14, 14, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/173 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl) `ZINC001584271978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584271978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584271978 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 4, 6, 13, 13, 13, 13, 13, 13, 10, 10, 10, 18, 18, 18, 10, 10, 4, 13, 13, 13, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584271978 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 Building ZINC001584271978 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584271978 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 172) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl) `ZINC001584271978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584271978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584271978 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 2, 10, 10, 1, 1, 1, 1, 5, 5, 5, 14, 14, 5, 9, 14, 14, 14, 14, 14, 14, 10, 10, 10, 19, 19, 19, 10, 10, 5, 14, 14, 14, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 173) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl) `ZINC001584271978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584271978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584271978 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)cc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 13, 13, 4, 6, 13, 13, 13, 13, 13, 13, 10, 10, 10, 18, 18, 18, 10, 10, 4, 13, 13, 13, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584271978 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584271978 Building ZINC001584513971 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584513971 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/174 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1) `ZINC001584513971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584513971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001584513971 none CCCCOc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 16, 10, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 3, 1, 6, 6, 44, 44, 44, 44, 44, 33, 33, 16, 16, 6, 6, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/175 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1) `ZINC001584513971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584513971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001584513971 none CCCCOc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 18, 10, 2, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 1, 6, 6, 47, 46, 46, 46, 46, 36, 36, 18, 18, 6, 6, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 6, 6] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584513971 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 Building ZINC001584513971 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584513971 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 174) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCOc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1) `ZINC001584513971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584513971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001584513971 none CCCCOc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 16, 10, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 3, 1, 6, 6, 44, 44, 44, 44, 44, 33, 33, 16, 16, 6, 6, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 6, 6] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 175) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCOc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1) `ZINC001584513971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584513971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001584513971 none CCCCOc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 18, 10, 2, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 1, 6, 6, 47, 46, 46, 46, 46, 36, 36, 18, 18, 6, 6, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 6, 6] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584513971 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584513971 Building ZINC001584518281 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584518281 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/176 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)CC1) `ZINC001584518281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584518281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584518281 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 37, 46, 46, 50, 50, 50, 50, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/177 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)CC1) `ZINC001584518281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584518281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584518281 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 37, 44, 44, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 58, 59, 60, 61] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584518281 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 Building ZINC001584518281 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584518281 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 176) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)CC1) `ZINC001584518281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584518281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584518281 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 37, 46, 46, 50, 50, 50, 50, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 177) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)CC1) `ZINC001584518281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584518281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584518281 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cccc(NC(=O)OC(C)(C)C)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 37, 44, 44, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 58, 59, 60, 61] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584518281 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584518281 Building ZINC001584522556 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584522556 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/178 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001584522556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584522556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584522556 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 50, 27, 8, 8, 25, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 25, 25, 8, 8, 2, 2, 1, 2, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/179 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001584522556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584522556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584522556 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 50, 27, 8, 8, 24, 24, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 24, 24, 8, 8, 2, 2, 1, 2, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584522556 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 Building ZINC001584522556 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584522556 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 178) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001584522556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584522556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584522556 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 50, 27, 8, 8, 25, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 25, 25, 8, 8, 2, 2, 1, 2, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 179) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001584522556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584522556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584522556 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 50, 27, 8, 8, 24, 24, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 27, 27, 24, 24, 8, 8, 2, 2, 1, 2, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584522556 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584522556 Building ZINC001584531690 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584531690 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/180 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Br)ccc(F)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001584531690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584531690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584531690 none O=C(N1CCc2c(Br)ccc(F)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 17, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 6, 1, 6] 49 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/181 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Br)ccc(F)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001584531690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584531690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584531690 none O=C(N1CCc2c(Br)ccc(F)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 17, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 1, 6] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584531690 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 Building ZINC001584531690 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584531690 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 180) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Br)ccc(F)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001584531690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584531690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584531690 none O=C(N1CCc2c(Br)ccc(F)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 17, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 6, 1, 6] 49 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 181) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Br)ccc(F)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001584531690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584531690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584531690 none O=C(N1CCc2c(Br)ccc(F)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 17, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 6, 1, 6] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584531690 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584531690 Building ZINC001584544299 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544299 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/182 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544299 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/183 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544299 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 6, 17, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 17, 17] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544299 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 Building ZINC001584544299 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544299 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 182) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544299 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 183) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544299 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 6, 17, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 17, 17] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544299 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544299 Building ZINC001584544300 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544300 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/184 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544300 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 13, 23, 13, 13, 13, 13, 4, 13, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/185 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544300 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 6, 15, 6, 7, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 15, 15] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544300 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 Building ZINC001584544300 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544300 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 184) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544300 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 13, 23, 13, 13, 13, 13, 4, 13, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 185) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544300 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 6, 15, 6, 7, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 15, 15] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544300 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544300 Building ZINC001584544302 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544302 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/186 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544302 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 25, 14, 14, 14, 14, 6, 14, 6, 7, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/187 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544302 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 19, 12, 12, 12, 12, 4, 12, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544302 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 Building ZINC001584544302 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544302 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 186) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544302 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 25, 14, 14, 14, 14, 6, 14, 6, 7, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 14, 14] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 187) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544302 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 19, 12, 12, 12, 12, 4, 12, 4, 5, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544302 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544302 Building ZINC001584544303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/188 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544303 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 23, 16, 23, 16, 16, 16, 16, 6, 16, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/189 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544303 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 Building ZINC001584544303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584544303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 188) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584544303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544303 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 23, 16, 23, 16, 16, 16, 16, 6, 16, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 189) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001584544303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584544303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001584544303 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 12, 3, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584544303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584544303 Building ZINC001584595567 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584595567 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/190 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584595567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595567 none O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/191 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584595567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595567 none O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584595567 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 Building ZINC001584595567 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584595567 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 190) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584595567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595567 none O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 191) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584595567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595567 none O=C(N[C@@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584595567 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595567 Building ZINC001584595568 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584595568 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/192 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584595568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595568 none O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/193 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584595568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595568 none O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584595568 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 Building ZINC001584595568 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584595568 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 192) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584595568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595568 none O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 193) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584595568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584595568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001584595568 none O=C(N[C@H](c1c[nH]c2cccc(F)c21)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 10, 5, 24, 24, 24, 24, 10, 10] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584595568 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584595568 Building ZINC001584648057 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584648057 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/194 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584648057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584648057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584648057 none O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 26, 26, 10, 26, 26, 26, 27, 29, 29, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 26, 26, 26, 26, 29, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/195 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584648057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584648057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584648057 none O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 28, 28, 10, 28, 28, 28, 29, 30, 30, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 28, 28, 28, 28, 30, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584648057 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 Building ZINC001584648057 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584648057 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 194) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584648057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584648057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584648057 none O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 26, 26, 10, 26, 26, 26, 27, 29, 29, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 26, 26, 26, 26, 29, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 195) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584648057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584648057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001584648057 none O=C(Nc1nc(c2ccccc2OC(F)F)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 28, 28, 10, 28, 28, 28, 29, 30, 30, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 28, 28, 28, 28, 30, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584648057 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584648057 Building ZINC001584791349 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584791349 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/196 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1) `ZINC001584791349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584791349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584791349 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 44, 49, 49, 49, 9, 9, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/197 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1) `ZINC001584791349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584791349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584791349 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 41, 47, 47, 47, 9, 9, 9, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584791349 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 Building ZINC001584791349 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584791349 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 196) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1) `ZINC001584791349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584791349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584791349 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 44, 49, 49, 49, 9, 9, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 3, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 197) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1) `ZINC001584791349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584791349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001584791349 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)(F)F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 41, 47, 47, 47, 9, 9, 9, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584791349 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584791349 Building ZINC001584801619 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584801619 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/198 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001584801619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584801619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001584801619 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 38, 48, 48, 48, 48, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 18, 18, 18, 18, 19, 19, 38, 38, 48, 48, 48, 19, 19, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/199 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001584801619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584801619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001584801619 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 18, 38, 48, 48, 48, 48, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 18, 18, 18, 18, 19, 19, 38, 38, 48, 48, 48, 19, 19, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584801619 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 Building ZINC001584801619 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584801619 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 198) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001584801619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584801619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001584801619 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 38, 48, 48, 48, 48, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 18, 18, 18, 18, 19, 19, 38, 38, 48, 48, 48, 19, 19, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 199) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001584801619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584801619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001584801619 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 18, 18, 18, 18, 18, 18, 19, 19, 18, 18, 38, 48, 48, 48, 48, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 2, 9, 9, 18, 18, 18, 18, 19, 19, 38, 38, 48, 48, 48, 19, 19, 4, 4] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584801619 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584801619 Building ZINC001584878994 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584878994 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/200 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584878994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584878994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584878994 none Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 13, 15, 15, 12, 8, 4, 8, 14, 21, 21, 21, 21, 21, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 12, 15, 15, 12, 12, 14, 14, 21, 21, 21, 21, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/201 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584878994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584878994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584878994 none Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 12, 8, 4, 8, 14, 21, 21, 21, 21, 21, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 12, 12, 14, 14, 21, 21, 21, 21, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584878994 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 Building ZINC001584878994 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584878994 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 200) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584878994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584878994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584878994 none Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 13, 15, 15, 12, 8, 4, 8, 14, 21, 21, 21, 21, 21, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 12, 15, 15, 12, 12, 14, 14, 21, 21, 21, 21, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 201) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001584878994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584878994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584878994 none Cc1ccccc1CN(Cc1ccccn1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 12, 8, 4, 8, 14, 21, 21, 21, 21, 21, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 12, 12, 14, 14, 21, 21, 21, 21, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584878994 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584878994 Building ZINC001584879055 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584879055 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/202 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001584879055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584879055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584879055 none Cc1cccc(CN(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 9, 8, 4, 8, 12, 15, 15, 15, 15, 15, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 9, 9, 12, 12, 15, 15, 15, 15, 4, 4, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/203 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001584879055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584879055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584879055 none Cc1cccc(CN(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 23, 23, 9, 8, 4, 8, 12, 16, 16, 16, 16, 16, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 23, 23, 18, 23, 23, 9, 9, 12, 12, 16, 16, 16, 16, 4, 4, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584879055 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 Building ZINC001584879055 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584879055 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 202) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001584879055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584879055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584879055 none Cc1cccc(CN(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 9, 8, 4, 8, 12, 15, 15, 15, 15, 15, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 9, 9, 12, 12, 15, 15, 15, 15, 4, 4, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 203) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001584879055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584879055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001584879055 none Cc1cccc(CN(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 23, 23, 9, 8, 4, 8, 12, 16, 16, 16, 16, 16, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 23, 23, 18, 23, 23, 9, 9, 12, 12, 16, 16, 16, 16, 4, 4, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584879055 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584879055 Building ZINC001584916470 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584916470 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/204 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl) `ZINC001584916470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584916470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584916470 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 12, 24, 24, 24, 6, 6, 6, 10, 10, 10, 6, 6, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/205 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl) `ZINC001584916470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584916470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584916470 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 24, 24, 24, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 12, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584916470 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 Building ZINC001584916470 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584916470 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 204) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl) `ZINC001584916470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584916470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584916470 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 12, 24, 24, 24, 6, 6, 6, 10, 10, 10, 6, 6, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 205) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl) `ZINC001584916470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584916470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584916470 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2cccc(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 24, 24, 24, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 6, 24, 24, 12, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584916470 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584916470 Building ZINC001584932668 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584932668 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/206 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C) `ZINC001584932668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584932668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584932668 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 13, 13, 13, 13, 13, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/207 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C) `ZINC001584932668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584932668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584932668 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 13, 13, 13, 13, 13, 9, 9, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 4, 16, 16, 8, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584932668 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 Building ZINC001584932668 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584932668 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 206) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C) `ZINC001584932668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584932668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584932668 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 13, 13, 13, 13, 13, 9, 9, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 207) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C) `ZINC001584932668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584932668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001584932668 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 4, 4, 4, 4, 16, 16, 8, 16, 16, 16, 13, 13, 13, 13, 13, 9, 9, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 4, 16, 16, 8, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584932668 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932668 Building ZINC001584932958 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584932958 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/208 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1) `ZINC001584932958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584932958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584932958 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 4, 9, 9, 8, 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]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/209 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1) `ZINC001584932958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584932958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584932958 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 17, 17, 8, 16, 17, 17, 24, 24, 24, 24, 24, 17, 17, 4, 9, 9, 8, 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]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584932958 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 Building ZINC001584932958 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584932958 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 208) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1) `ZINC001584932958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584932958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584932958 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 17, 17, 4, 9, 9, 8, 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]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 209) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1) `ZINC001584932958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584932958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001584932958 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 17, 17, 8, 16, 17, 17, 24, 24, 24, 24, 24, 17, 17, 4, 9, 9, 8, 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]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584932958 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584932958 Building ZINC001584973942 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584973942 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/210 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584973942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973942 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 35, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/211 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584973942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973942 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584973942 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 Building ZINC001584973942 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584973942 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 210) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584973942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973942 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 35, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 211) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584973942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973942 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584973942 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973942 Building ZINC001584973943 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584973943 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/212 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584973943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973943 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 24, 29, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/213 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584973943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973943 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 34, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584973943 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 Building ZINC001584973943 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584973943 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 212) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584973943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973943 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 24, 29, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 213) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001584973943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584973943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001584973943 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CC[C@H]2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 34, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584973943 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584973943 Building ZINC001584986061 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584986061 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/214 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584986061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986061 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 4, 5, 11, 11, 11, 11, 11, 19, 19, 19, 11, 11, 19, 19, 19, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 11, 11, 11, 11, 19, 19, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/215 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584986061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986061 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 18, 18, 18, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 18, 18, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584986061 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 Building ZINC001584986061 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584986061 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 214) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584986061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986061 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 4, 5, 11, 11, 11, 11, 11, 19, 19, 19, 11, 11, 19, 19, 19, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 11, 11, 11, 11, 19, 19, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 215) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584986061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986061 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 18, 18, 18, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 18, 18, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584986061 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986061 Building ZINC001584986063 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584986063 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/216 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584986063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986063 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 18, 18, 18, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 18, 18, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/217 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584986063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986063 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 19, 19, 19, 11, 19, 19, 19, 19, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 11, 11, 11, 11, 19, 19, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584986063 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 Building ZINC001584986063 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584986063 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 216) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584986063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986063 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 18, 18, 18, 9, 9, 18, 18, 18, 9, 9, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 18, 18, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 217) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl) `ZINC001584986063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584986063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584986063 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](c3cc(F)c(F)c(F)c3)C2(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 19, 19, 19, 11, 19, 19, 19, 19, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 11, 11, 11, 11, 19, 19, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001584986063 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001584986063 Building ZINC001585002571 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585002571 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/218 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585002571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585002571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001585002571 none CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 16, 16, 16, 16, 28, 28, 22, 28, 28, 28, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 18, 18, 18, 18, 18, 18, 18, 16, 28, 28, 28, 28, 6, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/219 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585002571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585002571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001585002571 none CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 16, 16, 16, 16, 26, 26, 16, 17, 26, 26, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 17, 17, 17, 17, 17, 17, 17, 16, 26, 26, 26, 26, 6, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585002571 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 Building ZINC001585002571 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585002571 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 218) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585002571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585002571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001585002571 none CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 16, 16, 16, 16, 28, 28, 22, 28, 28, 28, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 18, 18, 18, 18, 18, 18, 18, 16, 28, 28, 28, 28, 6, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 219) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585002571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585002571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001585002571 none CC(C)n1cnc(c2ccc(Cl)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 16, 16, 16, 16, 26, 26, 16, 17, 26, 26, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 17, 17, 17, 17, 17, 17, 17, 16, 26, 26, 26, 26, 6, 7, 8, 8, 7, 8, 8, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585002571 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585002571 Building ZINC001585015764 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585015764 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/220 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/220' -> `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)N1CCCc2c(Cl)ccc(Cl)c21) `ZINC001585015764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585015764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585015764 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 41 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/221 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/221' -> `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)N1CCCc2c(Cl)ccc(Cl)c21) `ZINC001585015764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585015764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585015764 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 12 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 24 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585015764 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 Building ZINC001585015764 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585015764 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 220) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21) `ZINC001585015764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585015764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585015764 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 41 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 221) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21) `ZINC001585015764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585015764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585015764 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)ccc(Cl)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 6, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 12 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 24 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585015764 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585015764 Building ZINC001585079207 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585079207 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/222 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585079207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079207 none CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 29, 9, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 9, 9, 6, 6, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/223 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585079207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079207 none CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 31, 10, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 10, 10, 6, 6, 2, 2, 2, 2, 2, 2, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585079207 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 Building ZINC001585079207 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585079207 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 222) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585079207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079207 none CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 29, 9, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 9, 9, 6, 6, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 223) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585079207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079207 none CC(C)(C)OC(=O)NCC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 31, 10, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 10, 10, 6, 6, 2, 2, 2, 2, 2, 2, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585079207 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079207 Building ZINC001585079208 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585079208 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/224 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585079208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079208 none CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 26, 38, 12, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 26, 12, 12, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/225 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585079208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079208 none CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 23, 34, 8, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 8, 8, 6, 6, 4, 4, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585079208 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 Building ZINC001585079208 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585079208 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 224) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585079208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079208 none CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 26, 38, 12, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 26, 12, 12, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 225) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001585079208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585079208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001585079208 none CC(C)(C)OC(=O)NCC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 23, 34, 8, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 8, 8, 6, 6, 4, 4, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585079208 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585079208 Building ZINC001585197490 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585197490 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/226 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(C(F)(F)F)cc1) `ZINC001585197490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585197490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001585197490 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 25, 26, 28, 43, 43, 31, 41, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 11, 11, 28, 28, 28, 28, 28, 28, 43, 43, 43, 43] 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: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/227 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(C(F)(F)F)cc1) `ZINC001585197490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585197490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001585197490 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 25, 24, 27, 44, 44, 31, 41, 44, 44, 44, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 11, 11, 27, 27, 27, 27, 27, 27, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585197490 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 Building ZINC001585197490 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585197490 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 226) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(C(F)(F)F)cc1) `ZINC001585197490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585197490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001585197490 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 25, 26, 28, 43, 43, 31, 41, 43, 43, 43, 43, 43, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 11, 11, 28, 28, 28, 28, 28, 28, 43, 43, 43, 43] 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: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 227) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(C(F)(F)F)cc1) `ZINC001585197490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585197490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001585197490 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 11, 25, 24, 27, 44, 44, 31, 41, 44, 44, 44, 44, 44, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 11, 11, 27, 27, 27, 27, 27, 27, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585197490 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585197490 Building ZINC001585231280 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585231280 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/228 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1) `ZINC001585231280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585231280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001585231280 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 14, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 22, 22, 22, 39, 39, 22, 31, 39, 39, 34, 34, 34, 34, 34, 14, 5, 5, 5, 5, 39, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/229 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1) `ZINC001585231280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585231280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001585231280 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 13, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 5, 20, 20, 20, 20, 20, 38, 38, 32, 32, 38, 38, 34, 34, 34, 34, 34, 13, 5, 5, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585231280 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 Building ZINC001585231280 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585231280 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 228) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1) `ZINC001585231280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585231280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001585231280 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 14, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 22, 22, 22, 22, 22, 39, 39, 22, 31, 39, 39, 34, 34, 34, 34, 34, 14, 5, 5, 5, 5, 39, 39, 39, 39] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 229) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1) `ZINC001585231280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585231280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001585231280 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 13, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 5, 20, 20, 20, 20, 20, 38, 38, 32, 32, 38, 38, 34, 34, 34, 34, 34, 13, 5, 5, 5, 5, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585231280 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585231280 Building ZINC001585398000 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585398000 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/230 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2c1) `ZINC001585398000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585398000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001585398000 none Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 37, 37, 37, 37, 37, 37, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 37, 37, 37, 37, 15, 15, 3, 8, 8, 33] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/231 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2c1) `ZINC001585398000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585398000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001585398000 none Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 36, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 36, 36, 36, 36, 15, 15, 3, 8, 8, 33] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585398000 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 Building ZINC001585398000 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585398000 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 230) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2c1) `ZINC001585398000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585398000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001585398000 none Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 37, 37, 37, 37, 37, 37, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 37, 37, 37, 37, 15, 15, 3, 8, 8, 33] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 231) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2c1) `ZINC001585398000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585398000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001585398000 none Cc1ccc2nc(c3ccc(F)cc3)c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 36, 36, 36, 36, 36, 36, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 36, 36, 36, 36, 15, 15, 3, 8, 8, 33] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585398000 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585398000 Building ZINC001585424379 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585424379 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/232 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585424379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424379 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 6, 6, 6, 6, 6, 6, 10, 20, 20, 10, 20, 20, 20, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 20, 20, 17, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/233 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585424379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424379 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 15, 23, 23, 18, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 8, 8, 8, 8, 8, 8, 15, 15, 23, 23, 21, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585424379 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 Building ZINC001585424379 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585424379 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 232) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585424379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424379 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 6, 6, 6, 6, 6, 6, 10, 20, 20, 10, 20, 20, 20, 6, 6, 6, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 20, 20, 17, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 233) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585424379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424379 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 15, 23, 23, 18, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 8, 8, 8, 8, 8, 8, 15, 15, 23, 23, 21, 23, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585424379 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424379 Building ZINC001585424381 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585424381 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/234 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585424381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424381 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 15, 22, 22, 18, 22, 22, 22, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 15, 15, 22, 22, 20, 22, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/235 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585424381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424381 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 10, 19, 19, 13, 19, 19, 19, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 19, 19, 17, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585424381 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 Building ZINC001585424381 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585424381 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 234) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585424381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424381 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 15, 22, 22, 18, 22, 22, 22, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 15, 15, 22, 22, 20, 22, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 235) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl) `ZINC001585424381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585424381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001585424381 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2Cc2ccccc2Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 10, 19, 19, 13, 19, 19, 19, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 19, 19, 17, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585424381 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585424381 Building ZINC001585497630 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585497630 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/236 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1) `ZINC001585497630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585497630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585497630 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 8, 17, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/237 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1) `ZINC001585497630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585497630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585497630 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 6, 6, 5, 6, 6, 6, 4, 6, 6, 5, 5, 16, 16, 16, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585497630 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 Building ZINC001585497630 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585497630 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 236) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1) `ZINC001585497630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585497630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585497630 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 8, 8, 8, 8, 8, 8, 5, 8, 8, 7, 8, 17, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 237) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1) `ZINC001585497630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585497630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001585497630 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Br)cc1)c1ccc(NC(C)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 5, 6, 6, 5, 6, 6, 6, 4, 6, 6, 5, 5, 16, 16, 16, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585497630 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585497630 Building ZINC001585514423 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585514423 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/238 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585514423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585514423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001585514423 none O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 7, 26, 26, 36, 50, 50, 50, 50, 26, 26, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [0, 1, 51, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/239 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585514423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585514423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001585514423 none O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 8, 27, 27, 30, 50, 50, 50, 50, 27, 27, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [0, 1, 51, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585514423 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 Building ZINC001585514423 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585514423 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 238) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585514423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585514423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001585514423 none O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 7, 26, 26, 36, 50, 50, 50, 50, 26, 26, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [0, 1, 51, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 239) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585514423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585514423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001585514423 none O=C(N1CCC(Cc2nc(C3CCCC3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 8, 27, 27, 30, 50, 50, 50, 50, 27, 27, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [0, 1, 51, 49, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585514423 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585514423 Building ZINC001585598838 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585598838 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/240 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585598838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598838 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 21, 44, 44, 50, 50, 44, 50, 50, 50, 21, 21, 21, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 48, 48, 48, 48, 48, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3, 21, 21, 21, 21] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/241 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585598838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598838 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 44, 19, 44, 44, 50, 50, 44, 50, 50, 50, 19, 19, 19, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 49, 49, 49, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585598838 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 Building ZINC001585598838 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585598838 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 240) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585598838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598838 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 21, 44, 44, 50, 50, 44, 50, 50, 50, 21, 21, 21, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 48, 48, 48, 48, 48, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3, 21, 21, 21, 21] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 241) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585598838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598838 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 44, 19, 44, 44, 50, 50, 44, 50, 50, 50, 19, 19, 19, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 49, 49, 49, 49, 49, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19, 19] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585598838 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598838 Building ZINC001585598839 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585598839 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/242 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585598839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598839 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 20, 44, 44, 48, 48, 48, 48, 48, 48, 20, 20, 20, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 20, 20] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/243 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585598839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598839 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 20, 43, 43, 48, 48, 48, 48, 48, 48, 20, 20, 20, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 20, 20] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585598839 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 Building ZINC001585598839 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585598839 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 242) grep: /scratch/xiaobo/11891/xbl-8058088.38/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@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585598839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598839 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 20, 44, 44, 48, 48, 48, 48, 48, 48, 20, 20, 20, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 20, 20] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 243) grep: /scratch/xiaobo/11891/xbl-8058088.38/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@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001585598839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585598839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001585598839 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 20, 43, 43, 48, 48, 48, 48, 48, 48, 20, 20, 20, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 20, 20, 20, 20] 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585598839 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585598839 Building ZINC001585603795 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585603795 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/244 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1) `ZINC001585603795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585603795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001585603795 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 45, 50, 50, 46, 50, 50, 50, 45, 19, 19, 19, 4, 3, 3, 3, 3, 19, 50, 50, 50, 50] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/245 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1) `ZINC001585603795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585603795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001585603795 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 44, 50, 50, 44, 44, 50, 50, 44, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50, 50] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585603795 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 Building ZINC001585603795 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585603795 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 244) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1) `ZINC001585603795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585603795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001585603795 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 45, 50, 50, 46, 50, 50, 50, 45, 19, 19, 19, 4, 3, 3, 3, 3, 19, 50, 50, 50, 50] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 245) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1) `ZINC001585603795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585603795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001585603795 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 20, 20, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 44, 50, 50, 44, 44, 50, 50, 44, 20, 20, 20, 4, 3, 3, 3, 3, 20, 50, 50, 50, 50] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585603795 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585603795 Building ZINC001585662608 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585662608 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/246 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/246' -> `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)N1CCc2ccc(Cl)c(Cl)c2C1) `ZINC001585662608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585662608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585662608 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 7, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 64 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/247 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/247' -> `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)N1CCc2ccc(Cl)c(Cl)c2C1) `ZINC001585662608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585662608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585662608 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 6, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 63 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585662608 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 Building ZINC001585662608 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585662608 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 246) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1) `ZINC001585662608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585662608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585662608 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 7, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18] 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]) total number of confs: 64 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 247) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1) `ZINC001585662608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585662608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001585662608 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(Cl)c(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 6, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 63 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585662608 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585662608 Building ZINC001585701407 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585701407 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/248 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001585701407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585701407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585701407 none Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 20, 4, 3, 1, 3, 20, 20] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/249 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001585701407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585701407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585701407 none Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 20, 4, 3, 1, 3, 20, 20] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585701407 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 Building ZINC001585701407 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585701407 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 248) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001585701407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585701407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585701407 none Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 20, 4, 3, 1, 3, 20, 20] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 249) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001585701407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585701407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585701407 none Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 38, 20, 4, 3, 1, 3, 20, 20] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585701407 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585701407 Building ZINC001585727161 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585727161 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/250 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1) `ZINC001585727161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585727161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585727161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/251 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1) `ZINC001585727161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585727161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585727161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585727161 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 Building ZINC001585727161 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585727161 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 250) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1) `ZINC001585727161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585727161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585727161 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 251) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1) `ZINC001585727161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585727161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585727161 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCCCCCc1nc(c2ccc(Cl)cc2)no1 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', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585727161 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585727161 Building ZINC001585766066 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585766066 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/252 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C) `ZINC001585766066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585766066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585766066 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 6, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/253 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C) `ZINC001585766066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585766066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585766066 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585766066 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 Building ZINC001585766066 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585766066 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 252) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C) `ZINC001585766066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585766066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585766066 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 6, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 253) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C) `ZINC001585766066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585766066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001585766066 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1Cc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585766066 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585766066 Building ZINC001585818220 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585818220 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/254 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001585818220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585818220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585818220 none Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 7, 5, 7, 13, 14, 14, 14, 14, 14, 14, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 13, 13, 14, 14, 14, 14, 5, 5, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/255 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001585818220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585818220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585818220 none Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 5, 8, 14, 15, 15, 14, 15, 15, 15, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 14, 14, 15, 15, 15, 15, 5, 5, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585818220 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 Building ZINC001585818220 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585818220 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 254) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001585818220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585818220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585818220 none Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 7, 5, 7, 13, 14, 14, 14, 14, 14, 14, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 13, 13, 14, 14, 14, 14, 5, 5, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 255) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001585818220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585818220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585818220 none Cc1cncc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 5, 8, 14, 15, 15, 14, 15, 15, 15, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 14, 14, 15, 15, 15, 15, 5, 5, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585818220 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585818220 Building ZINC001585822908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585822908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/256 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl) `ZINC001585822908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585822908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001585822908 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 14, 14, 14, 8, 8, 4, 12, 12, 12, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/257 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl) `ZINC001585822908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585822908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001585822908 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 8, 11, 11, 11, 8, 8, 8, 14, 14, 14, 8, 8, 4, 11, 11, 11, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585822908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 Building ZINC001585822908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585822908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 256) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl) `ZINC001585822908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585822908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001585822908 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 14, 14, 14, 8, 8, 4, 12, 12, 12, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 257) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl) `ZINC001585822908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585822908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001585822908 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(F)(F)F)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 8, 11, 11, 11, 8, 8, 8, 14, 14, 14, 8, 8, 4, 11, 11, 11, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585822908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585822908 Building ZINC001585838964 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585838964 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/258 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001585838964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585838964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585838964 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 39, 39, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/259 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001585838964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585838964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585838964 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 39, 39, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585838964 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 Building ZINC001585838964 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585838964 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 258) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001585838964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585838964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585838964 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 39, 39, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 259) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001585838964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585838964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585838964 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 8, 8, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 10, 10, 10, 10, 10, 4, 9, 39, 39, 9, 10, 10] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585838964 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585838964 Building ZINC001585886190 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585886190 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/260 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1) `ZINC001585886190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585886190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886190 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 26, 26, 26, 26, 8, 8, 8, 8, 21, 21, 18, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 21, 21, 21, 21, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/261 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1) `ZINC001585886190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585886190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886190 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 13, 13, 24, 24, 24, 24, 7, 7, 7, 7, 18, 18, 17, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585886190 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 Building ZINC001585886190 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585886190 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 260) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1) `ZINC001585886190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585886190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886190 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 26, 26, 26, 26, 8, 8, 8, 8, 21, 21, 18, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 21, 21, 21, 21, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 261) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1) `ZINC001585886190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585886190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886190 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 13, 13, 24, 24, 24, 24, 7, 7, 7, 7, 18, 18, 17, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585886190 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886190 Building ZINC001585886192 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585886192 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/262 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1) `ZINC001585886192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585886192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886192 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 14, 14, 24, 24, 24, 24, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 17, 17, 17, 17, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/263 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1) `ZINC001585886192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585886192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886192 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 7, 8, 8, 8, 8, 15, 15, 23, 24, 24, 24, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 24, 24, 24, 24, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 57, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585886192 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 Building ZINC001585886192 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585886192 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 262) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1) `ZINC001585886192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585886192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886192 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 14, 14, 24, 24, 24, 24, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 17, 17, 17, 17, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 2, 35, 57, 56, 4, 36, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 263) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1) `ZINC001585886192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585886192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001585886192 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 7, 8, 8, 8, 8, 15, 15, 23, 24, 24, 24, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 24, 24, 24, 24, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 57, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585886192 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585886192 Building ZINC001585919906 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585919906 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/264 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C) `ZINC001585919906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585919906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585919906 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 10, 10, 10, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 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: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/265 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C) `ZINC001585919906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585919906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585919906 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 6, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 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: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585919906 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 Building ZINC001585919906 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585919906 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 264) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C) `ZINC001585919906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585919906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585919906 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 10, 10, 10, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 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: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 265) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C) `ZINC001585919906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585919906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001585919906 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 6, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 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: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585919906 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585919906 Building ZINC001585931963 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585931963 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/266 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)c1) `ZINC001585931963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585931963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931963 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 14, 14, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/267 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)c1) `ZINC001585931963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585931963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931963 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 8, 8, 8, 8, 8, 8, 15, 15, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585931963 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 Building ZINC001585931963 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585931963 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 266) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)c1) `ZINC001585931963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585931963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931963 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 14, 14, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 267) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)c1) `ZINC001585931963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585931963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931963 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 8, 8, 8, 8, 8, 8, 15, 15, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585931963 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931963 Building ZINC001585931965 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585931965 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/268 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)c1) `ZINC001585931965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585931965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931965 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 1, 2, 2, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/269 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)c1) `ZINC001585931965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585931965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931965 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 7, 8, 8, 8, 8, 16, 16, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 2, 2, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 69 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585931965 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 Building ZINC001585931965 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585931965 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 268) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)c1) `ZINC001585931965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585931965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931965 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 1, 2, 2, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 269) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)c1) `ZINC001585931965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585931965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001585931965 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2ccccc2Cl)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 7, 8, 8, 8, 8, 16, 16, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 1, 2, 2, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 69 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585931965 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585931965 Building ZINC001585981800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585981800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/270 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585981800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585981800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585981800 none O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 33, 33, 6, 1, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/271 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585981800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585981800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585981800 none O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 33, 33, 6, 1, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585981800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 Building ZINC001585981800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585981800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 270) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585981800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585981800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585981800 none O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 33, 33, 6, 1, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 271) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001585981800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585981800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001585981800 none O=C(Nc1ncc(C(F)(F)F)cc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 8, 33, 33, 6, 1, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585981800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585981800 Building ZINC001585999120 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585999120 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/272 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585999120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585999120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585999120 none O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 14, 16, 16, 16, 8, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 4, 16, 14, 16, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/273 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585999120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585999120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585999120 none O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 8, 16, 16, 16, 8, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 4, 16, 8, 16, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585999120 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 Building ZINC001585999120 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585999120 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 272) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585999120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585999120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585999120 none O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 14, 16, 16, 16, 8, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 4, 16, 14, 16, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 273) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001585999120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585999120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001585999120 none O=C(Nc1nnc(c2cc(Cl)cc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 8, 16, 16, 16, 8, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 4, 16, 8, 16, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001585999120 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001585999120 Building ZINC001586168738 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586168738 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/274 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1) `ZINC001586168738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586168738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168738 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/275 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1) `ZINC001586168738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586168738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168738 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586168738 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 Building ZINC001586168738 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586168738 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 274) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1) `ZINC001586168738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586168738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168738 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 275) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1) `ZINC001586168738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586168738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168738 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586168738 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168738 Building ZINC001586168939 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586168939 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/276 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1) `ZINC001586168939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586168939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/277 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1) `ZINC001586168939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586168939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586168939 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 Building ZINC001586168939 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586168939 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 276) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1) `ZINC001586168939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586168939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 277) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1) `ZINC001586168939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586168939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586168939 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC/C=C\CCC1 NO_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', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586168939 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586168939 Building ZINC001586193888 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586193888 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/278 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586193888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586193888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001586193888 none O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 15, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 28, 48, 48, 48, 48, 48, 48, 48, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/279 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586193888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586193888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001586193888 none O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 15, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 28, 48, 48, 48, 48, 48, 48, 48, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586193888 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 Building ZINC001586193888 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586193888 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 278) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586193888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586193888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001586193888 none O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 15, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 28, 48, 48, 48, 48, 48, 48, 48, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 279) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586193888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586193888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001586193888 none O=C(Nc1ccc(Oc2cccc(F)c2F)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 15, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 28, 48, 48, 48, 48, 48, 48, 48, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586193888 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586193888 Building ZINC001586226683 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586226683 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/280 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586226683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586226683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001586226683 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 31, 31, 31, 30, 30, 31, 31, 31, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 31, 31, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/281 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586226683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586226683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001586226683 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 20, 20, 20, 20, 33, 33, 33, 31, 32, 33, 33, 33, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 20, 20, 33, 33, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586226683 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 Building ZINC001586226683 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586226683 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 280) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586226683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586226683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001586226683 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 31, 31, 31, 30, 30, 31, 31, 31, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 31, 31, 17, 17, 17, 17, 5, 5] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 281) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586226683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586226683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001586226683 none O=C(N1CCN(c2cc(Cl)c(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 16, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 20, 20, 20, 20, 33, 33, 33, 31, 32, 33, 33, 33, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 20, 20, 33, 33, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586226683 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586226683 Building ZINC001586253117 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586253117 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/282 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br) `ZINC001586253117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586253117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001586253117 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br NO_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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 13, 27, 27, 27, 27, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 4, 7, 27, 18, 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]) total number of confs: 112 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/283 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br) `ZINC001586253117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586253117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001586253117 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br NO_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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 7, 27, 27, 27, 27, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 27, 18, 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]) total number of confs: 119 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586253117 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 Building ZINC001586253117 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586253117 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 282) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br) `ZINC001586253117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586253117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001586253117 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br NO_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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 13, 27, 27, 27, 27, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 4, 7, 27, 18, 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]) total number of confs: 112 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 283) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br) `ZINC001586253117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586253117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001586253117 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(F)ccc(C)c1Br NO_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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 27, 27, 27, 7, 27, 27, 27, 27, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 27, 18, 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]) total number of confs: 119 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586253117 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586253117 Building ZINC001586284305 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586284305 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/284 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586284305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284305 none CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 35, 35, 35, 9, 8, 2, 9, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 35, 19, 19, 8, 8, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/285 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586284305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284305 none CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 20, 34, 34, 34, 10, 9, 4, 10, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586284305 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 Building ZINC001586284305 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586284305 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 284) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586284305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284305 none CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 35, 35, 35, 9, 8, 2, 9, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 35, 19, 19, 8, 8, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 285) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586284305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284305 none CCCC[C@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 20, 34, 34, 34, 10, 9, 4, 10, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586284305 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284305 Building ZINC001586284307 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586284307 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/286 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586284307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284307 none CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 35, 35, 35, 10, 10, 8, 10, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 35, 19, 19, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/287 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586284307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284307 none CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 20, 34, 34, 34, 9, 8, 4, 9, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586284307 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 Building ZINC001586284307 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586284307 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 286) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586284307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284307 none CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 35, 35, 35, 10, 10, 8, 10, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 35, 19, 19, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 287) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001586284307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586284307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586284307 none CCCC[C@@H](CC)COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 20, 34, 34, 34, 9, 8, 4, 9, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 34, 34, 34, 34, 34, 20, 20, 8, 8, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586284307 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586284307 Building ZINC001586299423 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586299423 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/288 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2) `ZINC001586299423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586299423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299423 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 1, 10, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 19, 19, 11, 19, 19, 11, 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/289 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2) `ZINC001586299423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586299423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299423 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 11, 11, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 11, 11, 9, 11, 11, 9, 8, 8, 8, 8, 8, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586299423 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 Building ZINC001586299423 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586299423 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 288) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2) `ZINC001586299423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586299423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299423 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 1, 10, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 19, 19, 11, 19, 19, 11, 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 289) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2) `ZINC001586299423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586299423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299423 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 11, 11, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 11, 11, 9, 11, 11, 9, 8, 8, 8, 8, 8, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586299423 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299423 Building ZINC001586299424 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586299424 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/290 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2) `ZINC001586299424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586299424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299424 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 10, 10, 10, 10, 10, 10, 10] 39 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]) total number of confs: 51 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/291 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2) `ZINC001586299424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586299424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299424 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 16, 16, 16, 16, 16, 11, 10, 10, 10, 10, 10, 10, 10] 48 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]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586299424 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 Building ZINC001586299424 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586299424 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 290) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2) `ZINC001586299424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586299424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299424 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 10, 10, 10, 10, 10, 10, 10] 39 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]) total number of confs: 51 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 291) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2) `ZINC001586299424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586299424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001586299424 none Cc1ccc(C(F)(F)F)c2c1N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', '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, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 16, 16, 16, 16, 16, 11, 10, 10, 10, 10, 10, 10, 10] 48 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]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586299424 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586299424 Building ZINC001586427498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586427498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/292 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586427498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427498 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 50, 50, 33, 33, 32, 24, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 24, 24, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/293 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586427498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427498 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 48, 48, 33, 33, 32, 22, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 33, 33, 33, 48, 48, 48, 48, 48, 33, 33, 33, 22, 22, 4, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586427498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 Building ZINC001586427498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586427498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 292) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586427498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427498 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 50, 50, 33, 33, 32, 24, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 24, 24, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 293) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586427498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427498 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 48, 48, 48, 33, 33, 32, 22, 32, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 32, 33, 33, 33, 48, 48, 48, 48, 48, 33, 33, 33, 22, 22, 4, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586427498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427498 Building ZINC001586427499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586427499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/294 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586427499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427499 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 34, 48, 48, 34, 34, 33, 23, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 34, 34, 34, 48, 48, 35, 48, 48, 34, 34, 34, 23, 23, 4, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/295 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586427499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427499 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 50, 35, 35, 33, 25, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 35, 35, 35, 50, 50, 35, 50, 50, 35, 35, 35, 25, 25, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586427499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 Building ZINC001586427499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586427499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 294) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586427499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427499 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 48, 34, 48, 48, 34, 34, 33, 23, 33, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 34, 34, 34, 48, 48, 35, 48, 48, 34, 34, 34, 23, 23, 4, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 295) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F) `ZINC001586427499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586427499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001586427499 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 50, 35, 35, 33, 25, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 35, 35, 35, 50, 50, 35, 50, 50, 35, 35, 35, 25, 25, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586427499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586427499 Building ZINC001586470244 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586470244 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/296 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1) `ZINC001586470244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586470244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586470244 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 10, 2, 2, 2, 2, 2, 10, 10, 35, 35] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/297 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1) `ZINC001586470244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586470244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586470244 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 3, 3, 3, 2, 2, 10, 10, 33, 33] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586470244 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 Building ZINC001586470244 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586470244 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 296) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1) `ZINC001586470244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586470244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586470244 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 10, 2, 2, 2, 2, 2, 10, 10, 35, 35] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 297) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1) `ZINC001586470244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586470244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586470244 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1nccc(c2sccc2Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 8, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 10, 3, 3, 3, 2, 2, 10, 10, 33, 33] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586470244 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586470244 Building ZINC001586472883 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586472883 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/298 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1) `ZINC001586472883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586472883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001586472883 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 31, 39, 39, 31, 39, 39, 10, 10, 10, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 10, 10, 39, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/299 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1) `ZINC001586472883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586472883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001586472883 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 2, 19, 33, 33, 23, 33, 33, 10, 10, 10, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 10, 10, 33, 33, 33, 33, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586472883 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 Building ZINC001586472883 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586472883 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 298) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1) `ZINC001586472883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586472883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001586472883 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 31, 39, 39, 31, 39, 39, 10, 10, 10, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 10, 10, 39, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 299) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1) `ZINC001586472883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586472883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001586472883 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccncc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 2, 19, 33, 33, 23, 33, 33, 10, 10, 10, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 10, 10, 33, 33, 33, 33, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586472883 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586472883 Building ZINC001586479094 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586479094 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/300 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21) `ZINC001586479094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586479094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001586479094 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 11, 2, 13, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 20, 20, 20] 38 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/301 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21) `ZINC001586479094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586479094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001586479094 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 11, 2, 13, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 20, 20, 20] 39 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]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586479094 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 Building ZINC001586479094 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586479094 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 300) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21) `ZINC001586479094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586479094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001586479094 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 11, 2, 13, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 20, 20, 20] 38 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 301) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21) `ZINC001586479094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586479094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001586479094 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 11, 2, 13, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 20, 20, 20] 39 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]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586479094 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586479094 Building ZINC001586490412 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586490412 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/302 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br) `ZINC001586490412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586490412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586490412 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br 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.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 49, 49, 49, 49, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 4, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/303 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br) `ZINC001586490412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586490412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586490412 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br 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.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 49, 49, 49, 49, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 4, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586490412 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 Building ZINC001586490412 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586490412 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 302) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br) `ZINC001586490412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586490412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586490412 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br 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.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 49, 49, 49, 49, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 4, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 303) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br) `ZINC001586490412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586490412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586490412 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(OC(F)(F)F)c(F)cc1Br 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.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 49, 49, 49, 49, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 4, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586490412 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490412 Building ZINC001586490726 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586490726 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/304 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001586490726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586490726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001586490726 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 46, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/305 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001586490726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586490726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001586490726 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 46, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586490726 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 Building ZINC001586490726 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586490726 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 304) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001586490726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586490726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001586490726 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 46, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 305) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001586490726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586490726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001586490726 none O=C(Nc1cc(OC(F)(F)F)c(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 12, 12, 12, 46, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586490726 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586490726 Building ZINC001586492552 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586492552 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/306 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001586492552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586492552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586492552 none Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 31, 31, 32, 32, 32, 32, 27, 27, 27, 27, 27, 27, 7, 3, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/307 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001586492552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586492552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586492552 none Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 7, 30, 30, 31, 31, 31, 31, 26, 26, 26, 26, 26, 26, 7, 3, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586492552 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 Building ZINC001586492552 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586492552 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 306) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001586492552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586492552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586492552 none Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 31, 31, 32, 32, 32, 32, 27, 27, 27, 27, 27, 27, 7, 3, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 307) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001586492552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586492552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586492552 none Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)c2C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 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, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 7, 30, 30, 31, 31, 31, 31, 26, 26, 26, 26, 26, 26, 7, 3, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586492552 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586492552 Building ZINC001586539596 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586539596 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/308 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586539596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586539596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001586539596 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/309 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586539596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586539596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001586539596 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586539596 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 Building ZINC001586539596 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586539596 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 308) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586539596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586539596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001586539596 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 309) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001586539596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586539596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001586539596 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 29, 35, 35, 35, 8, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586539596 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586539596 Building ZINC001586572155 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586572155 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/310 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586572155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572155 none C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 33, 33, 33, 33, 33, 10, 10, 10, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 19, 19, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/311 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586572155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572155 none C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 31, 31, 31, 31, 31, 13, 13, 13, 5, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 18, 18, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586572155 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 Building ZINC001586572155 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586572155 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 310) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586572155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572155 none C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 33, 33, 33, 33, 33, 10, 10, 10, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 19, 19, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 311) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586572155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572155 none C[C@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 31, 31, 31, 31, 31, 13, 13, 13, 5, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 18, 18, 31, 31, 31, 31, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586572155 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572155 Building ZINC001586572157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586572157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/312 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586572157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572157 none C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 30, 30, 30, 30, 30, 13, 13, 13, 5, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 17, 17, 30, 30, 30, 30, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/313 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586572157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572157 none C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 33, 33, 33, 33, 33, 10, 10, 10, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 19, 19, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586572157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 Building ZINC001586572157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586572157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 312) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586572157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572157 none C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 30, 30, 30, 30, 30, 13, 13, 13, 5, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 17, 17, 30, 30, 30, 30, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 313) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586572157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586572157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001586572157 none C[C@@]1(Cc2cccc(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 33, 33, 33, 33, 33, 10, 10, 10, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 19, 19, 33, 33, 33, 33, 10, 10, 10, 10, 10, 10, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586572157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586572157 Building ZINC001586582930 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582930 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/314 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1) `ZINC001586582930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582930 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 11, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/315 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1) `ZINC001586582930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582930 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582930 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 Building ZINC001586582930 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582930 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 314) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1) `ZINC001586582930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582930 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 11, 11, 11, 11, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 315) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1) `ZINC001586582930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582930 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582930 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582930 Building ZINC001586582931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/316 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1) `ZINC001586582931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582931 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/317 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1) `ZINC001586582931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582931 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 17, 18, 18, 18, 18, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 Building ZINC001586582931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 316) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1) `ZINC001586582931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582931 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 317) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1) `ZINC001586582931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582931 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 17, 18, 18, 18, 18, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582931 Building ZINC001586582932 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582932 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/318 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1) `ZINC001586582932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582932 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 8, 8, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/319 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1) `ZINC001586582932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582932 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 2, 9, 9, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582932 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 Building ZINC001586582932 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582932 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 318) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1) `ZINC001586582932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582932 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 8, 8, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 319) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1) `ZINC001586582932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582932 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 14, 14, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 2, 9, 9, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582932 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582932 Building ZINC001586582933 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582933 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/320 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1) `ZINC001586582933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582933 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/321 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1) `ZINC001586582933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582933 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582933 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 Building ZINC001586582933 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586582933 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 320) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1) `ZINC001586582933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586582933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582933 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 321) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1) `ZINC001586582933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586582933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586582933 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H]1C1CCCC1 NO_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', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586582933 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586582933 Building ZINC001586592864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586592864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/322 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CC2)c2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586592864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586592864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586592864 none O=C(N1CC2(CC2)c2ccc(Br)cc21)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/323 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CC2)c2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586592864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586592864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586592864 none O=C(N1CC2(CC2)c2ccc(Br)cc21)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586592864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 Building ZINC001586592864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586592864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 322) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CC2(CC2)c2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586592864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586592864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586592864 none O=C(N1CC2(CC2)c2ccc(Br)cc21)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 323) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CC2(CC2)c2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001586592864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586592864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001586592864 none O=C(N1CC2(CC2)c2ccc(Br)cc21)[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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8] 30 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586592864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586592864 Building ZINC001586653869 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586653869 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/324 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl) `ZINC001586653869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586653869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001586653869 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 5, 5, 5, 5, 20, 20, 5, 20, 20, 20, 10, 10, 10, 10, 10, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 20, 20, 9, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/325 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl) `ZINC001586653869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586653869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001586653869 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 21, 21, 5, 21, 21, 21, 9, 9, 9, 9, 9, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 5, 21, 21, 9, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586653869 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 Building ZINC001586653869 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586653869 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 324) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl) `ZINC001586653869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586653869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001586653869 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 5, 5, 5, 5, 20, 20, 5, 20, 20, 20, 10, 10, 10, 10, 10, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 20, 20, 9, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 325) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl) `ZINC001586653869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586653869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001586653869 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 21, 21, 5, 21, 21, 21, 9, 9, 9, 9, 9, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 5, 21, 21, 9, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586653869 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586653869 Building ZINC001586698966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586698966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/326 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586698966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698966 none O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 35, 35, 35, 41, 41, 35, 38, 41, 41, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 105, 41, 41, 41, 41, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/327 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586698966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698966 none O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 40, 40, 40, 44, 44, 40, 44, 44, 44, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 120, 44, 44, 44, 44, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586698966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 Building ZINC001586698966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586698966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 326) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586698966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698966 none O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 35, 35, 35, 41, 41, 35, 38, 41, 41, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 105, 41, 41, 41, 41, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 327) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586698966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698966 none O=C(N1CCC([C@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 40, 40, 40, 44, 44, 40, 44, 44, 44, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 120, 44, 44, 44, 44, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586698966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698966 Building ZINC001586698967 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586698967 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/328 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586698967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698967 none O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 36, 36, 36, 44, 44, 36, 43, 44, 44, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 108, 44, 44, 44, 44, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 286 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/329 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586698967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698967 none O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 41, 41, 41, 46, 46, 41, 41, 46, 46, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 123, 46, 46, 46, 46, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586698967 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 Building ZINC001586698967 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586698967 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 328) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586698967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698967 none O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 36, 36, 36, 44, 44, 36, 43, 44, 44, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 108, 44, 44, 44, 44, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 286 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 329) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001586698967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586698967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001586698967 none O=C(N1CCC([C@@H](O)c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 12, 12, 12, 12, 41, 41, 41, 46, 46, 41, 41, 46, 46, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 123, 46, 46, 46, 46, 12, 12, 12, 12, 3, 1, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586698967 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586698967 Building ZINC001586725021 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586725021 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/330 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586725021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725021 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 32, 25, 32, 25, 25, 25, 10, 25, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 25, 25, 4, 3, 1, 3, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/331 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586725021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725021 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [44, 44, 44, 44, 35, 27, 35, 27, 27, 27, 10, 27, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 3, 3, 1, 3, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586725021 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 Building ZINC001586725021 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586725021 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 330) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586725021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725021 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 32, 25, 32, 25, 25, 25, 10, 25, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 25, 25, 4, 3, 1, 3, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 331) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586725021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725021 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [44, 44, 44, 44, 35, 27, 35, 27, 27, 27, 10, 27, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 3, 3, 1, 3, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586725021 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725021 Building ZINC001586725022 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586725022 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/332 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586725022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725022 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 33, 24, 33, 24, 24, 24, 9, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 24, 3, 3, 1, 3, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/333 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586725022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725022 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [47, 47, 47, 47, 34, 21, 34, 21, 21, 21, 11, 21, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 21, 21, 4, 3, 1, 3, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586725022 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 Building ZINC001586725022 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586725022 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 332) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586725022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725022 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 33, 24, 33, 24, 24, 24, 9, 22, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 24, 24, 24, 24, 3, 3, 1, 3, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 333) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2) `ZINC001586725022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586725022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586725022 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C12CCCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [47, 47, 47, 47, 34, 21, 34, 21, 21, 21, 11, 21, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 21, 21, 4, 3, 1, 3, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586725022 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586725022 Building ZINC001586798356 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586798356 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/334 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/334' -> `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)Nc1cc2ccccc2nc1Br) `ZINC001586798356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586798356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586798356 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/335 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/335' -> `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)Nc1cc2ccccc2nc1Br) `ZINC001586798356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586798356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586798356 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586798356 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 Building ZINC001586798356 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586798356 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 334) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br) `ZINC001586798356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586798356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586798356 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 335) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br) `ZINC001586798356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586798356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586798356 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc2ccccc2nc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 4, 6, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 80 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586798356 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586798356 Building ZINC001586821634 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586821634 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/336 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br) `ZINC001586821634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586821634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586821634 none COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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: [42, 42, 21, 42, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 42, 42, 42, 21, 21, 21, 4, 4, 2, 4, 21, 21] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/337 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br) `ZINC001586821634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586821634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586821634 none COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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: [42, 42, 21, 42, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 42, 42, 42, 21, 21, 21, 4, 4, 1, 4, 21, 21] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586821634 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 Building ZINC001586821634 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586821634 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 336) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br) `ZINC001586821634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586821634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586821634 none COC(=O)c1c(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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: [42, 42, 21, 42, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 42, 42, 42, 21, 21, 21, 4, 4, 2, 4, 21, 21] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 337) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br) `ZINC001586821634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586821634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001586821634 none COC(=O)c1c(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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: [42, 42, 21, 42, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 21, 21, 21, 21, 42, 42, 42, 21, 21, 21, 4, 4, 1, 4, 21, 21] 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586821634 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586821634 Building ZINC001586870376 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586870376 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/338 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1) `ZINC001586870376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586870376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586870376 none CSc1cccc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 14, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 42, 42, 42, 42, 42, 25, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 42, 50, 50, 50, 42, 42, 42, 25, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 42] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/339 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1) `ZINC001586870376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586870376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586870376 none CSc1cccc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 14, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 42, 42, 42, 42, 42, 26, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 42, 50, 50, 50, 42, 42, 42, 26, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 42] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586870376 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 Building ZINC001586870376 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586870376 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 338) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CSc1cccc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1) `ZINC001586870376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586870376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586870376 none CSc1cccc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 14, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 42, 42, 42, 42, 42, 25, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 42, 50, 50, 50, 42, 42, 42, 25, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 42] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 339) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CSc1cccc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1) `ZINC001586870376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586870376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001586870376 none CSc1cccc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.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, 14, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 42, 42, 42, 42, 42, 26, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 42, 50, 50, 50, 42, 42, 42, 26, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 42] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586870376 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586870376 Building ZINC001586903790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586903790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/340 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2) `ZINC001586903790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586903790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001586903790 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 36, 48, 48, 48, 36, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 3, 1, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/341 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2) `ZINC001586903790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586903790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001586903790 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 36, 48, 48, 48, 36, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 3, 1, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586903790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 Building ZINC001586903790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586903790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 340) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2) `ZINC001586903790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586903790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001586903790 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 36, 48, 48, 48, 36, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 3, 1, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 341) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2) `ZINC001586903790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586903790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001586903790 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ncc2c(n1)-c1ccccc1SC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 36, 48, 48, 48, 36, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 3, 1, 3, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586903790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586903790 Building ZINC001586948703 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586948703 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/342 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001586948703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586948703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001586948703 none O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 25, 25, 18, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 25, 25, 18, 25, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/343 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001586948703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586948703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001586948703 none O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 24, 24, 9, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 24, 24, 9, 24, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586948703 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 Building ZINC001586948703 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586948703 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 342) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001586948703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586948703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001586948703 none O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 25, 25, 18, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 25, 25, 18, 25, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 343) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001586948703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586948703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001586948703 none O=C(Nc1nnc(c2cccc(C(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 24, 24, 9, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 24, 24, 9, 24, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586948703 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586948703 Building ZINC001586952966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586952966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/344 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1) `ZINC001586952966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586952966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586952966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 6, 11, 11, 11, 6, 13, 13, 13, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 6, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/345 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1) `ZINC001586952966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586952966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586952966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 13, 13, 13, 6, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 6, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586952966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 Building ZINC001586952966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586952966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 344) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1) `ZINC001586952966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586952966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586952966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 6, 11, 11, 11, 6, 13, 13, 13, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 6, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 345) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1) `ZINC001586952966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586952966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001586952966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 13, 13, 13, 6, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 6, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001586952966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001586952966 Building ZINC001587093041 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587093041 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/346 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587093041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587093041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001587093041 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 11, 23, 26, 6, 4, 2, 1, 2, 4, 5, 5, 4, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/347 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587093041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587093041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001587093041 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 10, 24, 26, 6, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587093041 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 Building ZINC001587093041 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587093041 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 346) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587093041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587093041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001587093041 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 11, 23, 26, 6, 4, 2, 1, 2, 4, 5, 5, 4, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 151 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 347) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587093041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587093041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001587093041 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 10, 24, 26, 6, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587093041 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587093041 Building ZINC001587151576 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587151576 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/348 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1) `ZINC001587151576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587151576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587151576 none Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 43, 43, 19, 17, 9, 17, 17, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 43, 43, 43, 43, 42, 43, 43, 19, 9, 2, 5, 5, 9, 9, 9, 9, 9, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/349 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1) `ZINC001587151576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587151576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587151576 none Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 43, 43, 19, 17, 9, 17, 17, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 43, 43, 43, 43, 34, 43, 43, 19, 9, 2, 5, 5, 9, 9, 9, 9, 9, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587151576 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 Building ZINC001587151576 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587151576 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 348) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1) `ZINC001587151576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587151576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587151576 none Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 43, 43, 19, 17, 9, 17, 17, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 43, 43, 43, 43, 42, 43, 43, 19, 9, 2, 5, 5, 9, 9, 9, 9, 9, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 349) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1) `ZINC001587151576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587151576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587151576 none Cc1cccc(NS(=O)(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 43, 43, 19, 17, 9, 17, 17, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 43, 43, 43, 43, 34, 43, 43, 19, 9, 2, 5, 5, 9, 9, 9, 9, 9, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587151576 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587151576 Building ZINC001587152047 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587152047 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/350 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl) `ZINC001587152047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587152047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152047 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 28, 30, 30, 30, 30, 30, 30, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 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]) total number of confs: 121 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/351 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl) `ZINC001587152047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587152047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152047 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 27, 29, 29, 29, 29, 29, 29, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 127 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587152047 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 Building ZINC001587152047 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587152047 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 350) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl) `ZINC001587152047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587152047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152047 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 28, 30, 30, 30, 30, 30, 30, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 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]) total number of confs: 121 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 351) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl) `ZINC001587152047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587152047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152047 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 27, 29, 29, 29, 29, 29, 29, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 127 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587152047 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152047 Building ZINC001587152048 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587152048 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/352 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl) `ZINC001587152048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587152048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152048 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 25, 27, 27, 27, 27, 27, 27, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 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]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/353 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl) `ZINC001587152048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587152048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152048 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 13, 28, 31, 31, 28, 31, 31, 31, 3, 3, 3, 10, 10, 9, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587152048 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 Building ZINC001587152048 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587152048 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 352) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl) `ZINC001587152048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587152048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152048 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 25, 27, 27, 27, 27, 27, 27, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 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]) total number of confs: 115 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 353) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl) `ZINC001587152048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587152048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587152048 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 4, 7, 13, 13, 13, 13, 13, 13, 28, 31, 31, 28, 31, 31, 31, 3, 3, 3, 10, 10, 9, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587152048 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587152048 Building ZINC001587225100 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225100 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/354 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225100 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 34, 46, 46, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/355 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225100 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 35, 48, 48, 48, 48, 48, 48, 4, 2, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 4, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225100 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 Building ZINC001587225100 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225100 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 354) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225100 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 34, 46, 46, 50, 50, 50, 50, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 355) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225100 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 35, 48, 48, 48, 48, 48, 48, 4, 2, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 4, 1, 4, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225100 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225100 Building ZINC001587225101 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225101 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/356 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225101 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 27, 38, 38, 43, 43, 43, 43, 6, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/357 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225101 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 20, 34, 45, 45, 50, 50, 50, 50, 6, 3, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 8, 8, 8] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225101 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 Building ZINC001587225101 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225101 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 356) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225101 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 27, 38, 38, 43, 43, 43, 43, 6, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 357) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C) `ZINC001587225101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225101 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 20, 34, 45, 45, 50, 50, 50, 50, 6, 3, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 8, 8, 8] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225101 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225101 Building ZINC001587225102 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225102 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/358 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225102 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 42, 42, 48, 48, 48, 48, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/359 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225102 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 35, 44, 44, 49, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225102 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 Building ZINC001587225102 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225102 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 358) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225102 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 42, 42, 48, 48, 48, 48, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 359) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225102 none C[C@@H]1CC[C@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 35, 44, 44, 49, 49, 49, 49, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [17, 19, 21, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225102 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225102 Building ZINC001587225103 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225103 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/360 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225103 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 16, 30, 40, 40, 50, 50, 50, 50, 6, 3, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 8, 8, 8] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/361 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225103 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 28, 39, 39, 47, 47, 47, 47, 6, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225103 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 Building ZINC001587225103 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587225103 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 360) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587225103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225103 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 16, 30, 40, 40, 50, 50, 50, 50, 6, 3, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 8, 8, 8] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 361) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C) `ZINC001587225103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587225103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001587225103 none C[C@@H]1CC[C@@H](CNC(=O)OC(C)(C)C)N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 28, 39, 39, 47, 47, 47, 47, 6, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 1, 3, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587225103 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587225103 Building ZINC001587226437 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587226437 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/362 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1) `ZINC001587226437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587226437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001587226437 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1 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.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 17, 28, 17, 17, 17, 17, 10, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3, 3, 17, 17, 17, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/363 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1) `ZINC001587226437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587226437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001587226437 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1 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.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 18, 29, 18, 18, 18, 18, 10, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587226437 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 Building ZINC001587226437 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587226437 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 362) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1) `ZINC001587226437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587226437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001587226437 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1 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.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 17, 28, 17, 17, 17, 17, 10, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3, 3, 17, 17, 17, 17] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 363) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1) `ZINC001587226437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587226437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001587226437 none CC(C)(C)OC(=O)N1CCc2c(F)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2C1 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.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 18, 29, 18, 18, 18, 18, 10, 18, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18] 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587226437 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587226437 Building ZINC001587227336 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587227336 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/364 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/365 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/366 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/366' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/367 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/367' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587227336 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 Building ZINC001587227336 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587227336 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 364) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 365) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 366) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 367) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587227336 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 Building ZINC001587227336 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587227336 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 364) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 365) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 366) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 367) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587227336 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 Building ZINC001587227336 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587227336 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 364) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 365) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 366) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 367) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587227336.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587227336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001587227336 none O=C(Nc1ccc2c(c1)N(CC(F)F)CCS2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 5, 5, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 23, 23, 23, 12, 23, 23, 32, 34, 34, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 3, 23, 23, 23, 32, 32, 34, 23, 23, 23, 23, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587227336 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587227336 Building ZINC001587252846 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252846 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/368 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/369 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/370 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/370' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/371 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/371' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252846 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 Building ZINC001587252846 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252846 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 368) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 369) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 370) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 371) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252846 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 Building ZINC001587252846 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252846 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 368) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 369) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 370) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 371) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252846 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 Building ZINC001587252846 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252846 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 368) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 369) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 216 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 370) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 371) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252846.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252846 none CN(CCC(F)(F)F)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 35, 35, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252846 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252846 Building ZINC001587252847 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252847 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/372 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/373 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/374 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/374' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/375 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/375' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252847 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 Building ZINC001587252847 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252847 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 372) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 373) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 374) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 375) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252847 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 Building ZINC001587252847 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252847 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 372) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 373) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 374) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 375) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252847 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 Building ZINC001587252847 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587252847 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 372) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 373) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 50, 50, 50, 50, 50, 15, 35, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 37, 37, 37, 37, 37, 37, 44, 44, 44, 50, 50, 50, 50, 15, 15, 2, 3, 3, 3, 3, 37, 37, 37, 37] 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]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 374) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 375) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1) `ZINC001587252847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587252847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001587252847 none CN(CCC(F)(F)F)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 15, 15, 15, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 46, 49, 50, 50, 50, 50, 16, 33, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 39, 39, 39, 39, 39, 39, 46, 46, 46, 49, 49, 50, 50, 16, 16, 3, 3, 3, 3, 3, 39, 39, 39, 39] 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]) total number of confs: 219 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587252847 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587252847 Building ZINC001587262982 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587262982 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/376 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587262982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587262982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587262982 none O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 35, 48, 48, 48, 48, 48, 48, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 19, 19, 48, 48, 42, 48, 9, 9, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/377 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587262982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587262982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587262982 none O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 15, 49, 49, 27, 49, 49, 49, 49, 49, 49, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 15, 15, 49, 49, 29, 49, 8, 8, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587262982 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 Building ZINC001587262982 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587262982 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 376) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587262982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587262982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587262982 none O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 35, 48, 48, 48, 48, 48, 48, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 19, 19, 48, 48, 42, 48, 9, 9, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 377) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587262982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587262982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587262982 none O=C(N1CCN(Cc2cccc(C(F)(F)F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 8, 8, 8, 8, 15, 49, 49, 27, 49, 49, 49, 49, 49, 49, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 15, 15, 49, 49, 29, 49, 8, 8, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587262982 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587262982 Building ZINC001587352894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587352894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/378 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587352894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587352894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001587352894 none O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 10, 10, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 44, 44, 44, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/379 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587352894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587352894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001587352894 none O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 43, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 44, 44, 44, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587352894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 Building ZINC001587352894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587352894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 378) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587352894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587352894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001587352894 none O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 10, 10, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 44, 44, 44, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 379) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001587352894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587352894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001587352894 none O=C(NCc1ccc(Cl)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 43, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 44, 44, 44, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587352894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587352894 Building ZINC001587370013 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587370013 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/380 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC001587370013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587370013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001587370013 none Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 11, 11, 4, 4, 4, 2, 2, 4, 2, 2, 50, 50, 50, 50] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/381 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC001587370013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587370013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001587370013 none Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 11, 11, 4, 4, 4, 2, 2, 4, 2, 2, 50, 50, 50, 50] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587370013 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 Building ZINC001587370013 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587370013 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 380) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC001587370013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587370013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001587370013 none Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 11, 11, 4, 4, 4, 2, 2, 4, 2, 2, 50, 50, 50, 50] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 381) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C) `ZINC001587370013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587370013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001587370013 none Cc1ccc(c2nn(c3ccccc3)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 11, 11, 4, 4, 4, 2, 2, 4, 2, 2, 50, 50, 50, 50] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587370013 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587370013 Building ZINC001587423841 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587423841 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/382 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001587423841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587423841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001587423841 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 7, 30, 30, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/383 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001587423841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587423841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001587423841 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 7, 30, 30, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587423841 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 Building ZINC001587423841 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587423841 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 382) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001587423841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587423841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001587423841 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 7, 30, 30, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 383) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001587423841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587423841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001587423841 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'I', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 7, 30, 30, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587423841 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587423841 Building ZINC001587434943 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587434943 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/384 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587434943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434943 none O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 15, 15, 44, 44, 33, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 44, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/385 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587434943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434943 none O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 14, 14, 14, 14, 14, 14, 14, 42, 42, 30, 42, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 42, 42, 32, 42, 3, 1, 3] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587434943 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 Building ZINC001587434943 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587434943 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 384) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587434943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434943 none O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 15, 15, 44, 44, 33, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 44, 44, 44, 44, 3, 1, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 385) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587434943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434943 none O=C(N1CCOC[C@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 14, 14, 14, 14, 14, 14, 14, 42, 42, 30, 42, 42, 42, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 42, 42, 32, 42, 3, 1, 3] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587434943 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434943 Building ZINC001587434944 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587434944 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/386 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587434944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434944 none O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 15, 15, 15, 15, 15, 15, 15, 49, 49, 36, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 49, 49, 49, 49, 3, 1, 3] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/387 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587434944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434944 none O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 16, 16, 44, 44, 31, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 44, 44, 43, 44, 3, 3, 3] 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]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587434944 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 Building ZINC001587434944 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587434944 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 386) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587434944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434944 none O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 15, 15, 15, 15, 15, 15, 15, 49, 49, 36, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 49, 49, 49, 49, 3, 1, 3] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 387) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587434944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587434944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001587434944 none O=C(N1CCOC[C@@H]1c1cccc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 16, 16, 16, 16, 16, 16, 16, 44, 44, 31, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 44, 44, 43, 44, 3, 3, 3] 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]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587434944 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587434944 Building ZINC001587484929 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587484929 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/388 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587484929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484929 none O=C(C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 26, 32, 32, 26, 32, 32, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 32, 32, 32, 32, 32] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/389 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587484929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484929 none O=C(C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 35, 41, 41, 40, 41, 41, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 41, 41, 41, 41, 41] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587484929 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 Building ZINC001587484929 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587484929 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 388) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587484929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484929 none O=C(C[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 26, 32, 32, 26, 32, 32, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 32, 32, 32, 32, 32] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 389) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587484929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484929 none O=C(C[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 35, 41, 41, 40, 41, 41, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 41, 41, 41, 41, 41] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587484929 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484929 Building ZINC001587484931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587484931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/390 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587484931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484931 none O=C(C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 36, 40, 40, 40, 40, 40, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/391 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587484931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484931 none O=C(C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 28, 34, 34, 28, 34, 34, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 34, 34, 34, 34, 34] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587484931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 Building ZINC001587484931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587484931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 390) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587484931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484931 none O=C(C[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 36, 40, 40, 40, 40, 40, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 391) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001587484931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587484931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587484931 none O=C(C[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 28, 34, 34, 28, 34, 34, 15, 15, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 34, 34, 34, 34, 34] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587484931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587484931 Building ZINC001587486251 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587486251 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/392 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl) `ZINC001587486251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587486251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001587486251 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 19, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 20, 20, 20, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/393 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl) `ZINC001587486251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587486251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001587486251 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 16, 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] 0 hydrogens 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, 4, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 19, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 20, 20, 20, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587486251 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 Building ZINC001587486251 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587486251 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 392) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl) `ZINC001587486251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587486251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001587486251 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 19, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 20, 20, 20, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 393) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl) `ZINC001587486251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587486251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001587486251 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)c2nc3cc(Br)ccc3s2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 16, 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] 0 hydrogens 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, 4, 5, 5, 1, 1, 1, 1, 3, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 19, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 20, 20, 20, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587486251 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587486251 Building ZINC001587524015 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587524015 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/394 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2) `ZINC001587524015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587524015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001587524015 none CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 20, 31, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 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: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/395 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2) `ZINC001587524015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587524015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001587524015 none CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 18, 29, 5, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 5, 5, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 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: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587524015 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 Building ZINC001587524015 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587524015 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 394) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2) `ZINC001587524015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587524015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001587524015 none CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 20, 31, 6, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 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: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 395) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2) `ZINC001587524015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587524015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001587524015 none CC(C)(C)OC(=O)NCc1cccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 18, 29, 5, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 5, 5, 2, 2, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 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: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587524015 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587524015 Building ZINC001587564460 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587564460 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/396 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/396' -> `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)Nc1scnc1C(C)C) `ZINC001587564460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587564460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587564460 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1scnc1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 25, 25, 6, 25, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/397 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/397' -> `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)Nc1scnc1C(C)C) `ZINC001587564460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587564460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587564460 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1scnc1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587564460 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 Building ZINC001587564460 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587564460 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 396) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1scnc1C(C)C) `ZINC001587564460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587564460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587564460 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1scnc1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 25, 25, 6, 25, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 397) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1scnc1C(C)C) `ZINC001587564460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587564460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587564460 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1scnc1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 14, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587564460 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587564460 Building ZINC001587611046 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587611046 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/398 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O) `ZINC001587611046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587611046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587611046 none CCN1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 43, 44, 44, 26, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 44, 44, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/399 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O) `ZINC001587611046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587611046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587611046 none CCN1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 44, 44, 44, 25, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 44, 44, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587611046 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 Building ZINC001587611046 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587611046 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 398) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O) `ZINC001587611046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587611046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587611046 none CCN1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 43, 44, 44, 26, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 26, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 44, 44, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 399) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O) `ZINC001587611046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587611046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001587611046 none CCN1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2OCC(C)(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens 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, 44, 44, 44, 44, 25, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 44, 44, 3, 3, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587611046 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587611046 Building ZINC001587784971 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587784971 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/400 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1) `ZINC001587784971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587784971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587784971 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/401 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1) `ZINC001587784971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587784971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587784971 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 47, 48, 48, 47, 48, 48, 48, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 48, 48, 48, 48, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587784971 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 Building ZINC001587784971 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587784971 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 400) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1) `ZINC001587784971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587784971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587784971 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 401) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1) `ZINC001587784971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587784971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001587784971 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 17, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 47, 48, 48, 47, 48, 48, 48, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 48, 48, 48, 48, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587784971 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587784971 Building ZINC001587900787 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900787 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/402 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/403 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/404 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/404' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/405 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/405' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900787 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 Building ZINC001587900787 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900787 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 402) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 403) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 404) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 405) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900787 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 Building ZINC001587900787 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900787 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 402) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 403) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 404) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 405) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900787 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 Building ZINC001587900787 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900787 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 402) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 403) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 46, 46, 38, 46, 46, 23, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 38, 38, 46, 46, 38, 46, 46, 23, 23, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 404) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 405) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900787 none O=C(N1CC[C@@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 47, 47, 37, 47, 47, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 37, 37, 47, 47, 37, 47, 47, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900787 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900787 Building ZINC001587900788 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900788 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/406 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/407 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/408 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/408' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/409 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/409' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900788 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 Building ZINC001587900788 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900788 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 406) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 407) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 408) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 409) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900788 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 Building ZINC001587900788 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900788 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 406) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 407) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 408) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 409) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900788 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 Building ZINC001587900788 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900788 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 406) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 407) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 44, 44, 34, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 44, 44, 34, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 408) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 409) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900788 none O=C(N1CC[C@@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 2, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 48, 48, 35, 48, 48, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 48, 48, 35, 48, 48, 20, 20, 3, 2, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900788 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900788 Building ZINC001587900789 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900789 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/410 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/411 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/412 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/412' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/413 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/413' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900789 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 Building ZINC001587900789 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900789 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 410) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 411) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 412) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 413) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900789 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 Building ZINC001587900789 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900789 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 410) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 411) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 412) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 413) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900789 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 Building ZINC001587900789 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900789 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 410) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 411) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 47, 47, 38, 47, 47, 21, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 47, 47, 38, 47, 47, 21, 21, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 412) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 413) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900789 none O=C(N1CC[C@H]2[C@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 2, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 44, 44, 35, 44, 44, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 35, 35, 44, 44, 35, 44, 44, 17, 17, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900789 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900789 Building ZINC001587900790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/414 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/415 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/416 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/416' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/417 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/417' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 Building ZINC001587900790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 414) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 415) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 416) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 417) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 Building ZINC001587900790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 414) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 415) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 416) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 417) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 Building ZINC001587900790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001587900790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 414) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 415) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 46, 46, 36, 46, 46, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 46, 46, 36, 46, 46, 22, 22, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 416) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 417) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001587900790.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001587900790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001587900790 none O=C(N1CC[C@H]2[C@@H](CCCN2Cc2ccccc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 46, 46, 37, 46, 46, 24, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 46, 46, 37, 46, 46, 24, 24, 3, 1, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587900790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587900790 Building ZINC001587925167 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587925167 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/418 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)nc(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1) `ZINC001587925167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587925167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001587925167 none COc1ccc2c(c1)nc(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 5, 5, 15, 21, 21, 18, 21, 21, 8, 8, 8, 5, 5, 5, 2, 8, 8, 15, 15, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/419 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)nc(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1) `ZINC001587925167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587925167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001587925167 none COc1ccc2c(c1)nc(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 5, 5, 15, 21, 21, 17, 21, 21, 8, 8, 8, 5, 5, 5, 2, 8, 8, 15, 15, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587925167 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 Building ZINC001587925167 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587925167 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 418) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc2c(c1)nc(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1) `ZINC001587925167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587925167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001587925167 none COc1ccc2c(c1)nc(NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 5, 5, 15, 21, 21, 18, 21, 21, 8, 8, 8, 5, 5, 5, 2, 8, 8, 15, 15, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 419) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc2c(c1)nc(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1) `ZINC001587925167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587925167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001587925167 none COc1ccc2c(c1)nc(NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)n2Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 5, 5, 15, 21, 21, 17, 21, 21, 8, 8, 8, 5, 5, 5, 2, 8, 8, 15, 15, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587925167 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587925167 Building ZINC001587982781 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587982781 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/420 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001587982781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587982781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001587982781 none COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 10, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 15, 15, 5, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/421 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001587982781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587982781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001587982781 none COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 10, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 15, 15, 5, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587982781 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 Building ZINC001587982781 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587982781 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 420) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001587982781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587982781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001587982781 none COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 10, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 15, 15, 5, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 421) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001587982781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587982781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001587982781 none COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 15, 15, 15, 10, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 15, 15, 5, 8, 8, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587982781 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587982781 Building ZINC001587998477 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587998477 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/422 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587998477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998477 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 18, 16, 17] set([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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/423 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587998477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998477 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 7, 27, 33, 33, 32, 32, 33, 33, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 7, 7, 7, 7, 33, 33, 33, 33, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587998477 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 Building ZINC001587998477 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587998477 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 422) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587998477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998477 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 18, 16, 17] set([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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 423) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587998477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998477 none O=C(N1CC[C@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 7, 7, 7, 7, 7, 27, 33, 33, 32, 32, 33, 33, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 7, 7, 7, 7, 33, 33, 33, 33, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587998477 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998477 Building ZINC001587998478 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587998478 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/424 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587998478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998478 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 7, 7, 7, 7, 7, 25, 30, 30, 25, 27, 30, 30, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/425 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587998478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998478 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 8, 8, 23, 29, 29, 23, 23, 29, 29, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 29, 29, 29, 29, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587998478 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 Building ZINC001587998478 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587998478 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 424) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587998478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998478 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 7, 7, 7, 7, 7, 25, 30, 30, 25, 27, 30, 30, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 30, 30, 30, 30, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 425) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001587998478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587998478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001587998478 none O=C(N1CC[C@@H](Sc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 8, 8, 8, 8, 8, 23, 29, 29, 23, 23, 29, 29, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 29, 29, 29, 29, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001587998478 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001587998478 Building ZINC001588005512 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588005512 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/426 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/426' -> `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)NCC(C)(C)CC(F)(F)F) `ZINC001588005512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588005512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588005512 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 11, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/427 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/427' -> `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)NCC(C)(C)CC(F)(F)F) `ZINC001588005512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588005512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588005512 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 11, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588005512 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 Building ZINC001588005512 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588005512 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 426) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F) `ZINC001588005512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588005512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588005512 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 11, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 427) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F) `ZINC001588005512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588005512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588005512 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 11, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588005512 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588005512 Building ZINC001588036489 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588036489 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/428 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001588036489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588036489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001588036489 none C=Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 11, 11, 9, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 12, 12, 12, 11, 11, 9, 9, 6, 6, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/429 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001588036489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588036489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001588036489 none C=Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 9, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 10, 10, 12, 12, 12, 10, 10, 9, 9, 6, 6, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588036489 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 Building ZINC001588036489 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588036489 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 428) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C=Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001588036489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588036489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001588036489 none C=Cc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 11, 11, 9, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 12, 12, 12, 11, 11, 9, 9, 6, 6, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 429) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C=Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001588036489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588036489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001588036489 none C=Cc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 9, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 10, 10, 12, 12, 12, 10, 10, 9, 9, 6, 6, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588036489 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588036489 Building ZINC001588145136 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145136 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/430 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/431 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/432 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/432' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/433 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/433' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145136 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 Building ZINC001588145136 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145136 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 430) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 431) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 432) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 433) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145136 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 Building ZINC001588145136 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145136 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 430) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 431) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 432) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 433) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145136 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 Building ZINC001588145136 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145136 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 430) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 431) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 32, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 32, 32, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 3, 3, 3, 3] 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, 57, 58, 59, 60]) total number of confs: 239 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 432) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 433) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145136 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 36, 50, 50, 50, 50, 50, 50, 7, 7, 6, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 36, 36, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 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, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145136 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145136 Building ZINC001588145137 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145137 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/434 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/435 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/436 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/436' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/437 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/437' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145137 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 Building ZINC001588145137 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145137 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 434) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 435) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 436) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 437) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145137 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 Building ZINC001588145137 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145137 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 434) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 435) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 436) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 437) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145137 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 Building ZINC001588145137 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001588145137 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 434) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 435) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 17, 27, 47, 50, 50, 47, 50, 50, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 17, 17, 27, 27, 47, 47, 50, 50, 47, 50, 50, 3, 3, 3, 3, 2, 2, 2, 2] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 436) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 437) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001588145137.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001588145137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001588145137 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 17, 27, 43, 50, 50, 43, 50, 50, 4, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17, 27, 27, 43, 43, 50, 50, 43, 50, 50, 4, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 246 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588145137 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588145137 Building ZINC001588197852 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588197852 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/438 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl) `ZINC001588197852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588197852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001588197852 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl 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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 45, 45, 47, 50, 50, 47, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 18, 18, 47, 47, 47, 47, 47, 47, 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/439 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl) `ZINC001588197852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588197852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001588197852 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl 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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 46, 45, 47, 50, 50, 47, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 18, 18, 47, 47, 47, 47, 47, 47, 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588197852 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 Building ZINC001588197852 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588197852 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 438) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl) `ZINC001588197852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588197852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001588197852 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl 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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 45, 45, 47, 50, 50, 47, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 18, 18, 47, 47, 47, 47, 47, 47, 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 439) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl) `ZINC001588197852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588197852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001588197852 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccc(Br)cc1Cl 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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 18, 46, 45, 47, 50, 50, 47, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 18, 18, 47, 47, 47, 47, 47, 47, 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588197852 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588197852 Building ZINC001588213805 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588213805 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/440 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F) `ZINC001588213805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588213805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/441 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F) `ZINC001588213805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588213805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588213805 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 Building ZINC001588213805 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588213805 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 440) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F) `ZINC001588213805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588213805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 441) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F) `ZINC001588213805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588213805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213805 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588213805 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213805 Building ZINC001588213806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588213806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/442 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F) `ZINC001588213806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588213806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213806 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/443 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F) `ZINC001588213806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588213806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213806 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588213806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 Building ZINC001588213806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588213806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 442) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F) `ZINC001588213806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588213806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213806 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 443) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F) `ZINC001588213806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588213806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588213806 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCC1(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588213806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588213806 Building ZINC001588267873 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588267873 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/444 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588267873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588267873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001588267873 none CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 6, 18, 18, 12, 18, 18, 18, 18, 18, 18, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 18, 14, 18, 5, 7, 7, 5, 7, 7, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/445 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588267873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588267873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001588267873 none CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 4, 9, 28, 28, 16, 28, 28, 28, 28, 28, 27, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 28, 28, 16, 28, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588267873 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 Building ZINC001588267873 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588267873 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 444) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588267873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588267873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001588267873 none CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 6, 18, 18, 12, 18, 18, 18, 18, 18, 18, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 18, 18, 14, 18, 5, 7, 7, 5, 7, 7, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 445) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588267873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588267873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001588267873 none CC(C)CN(Cc1cccc(C(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 4, 9, 28, 28, 16, 28, 28, 28, 28, 28, 27, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 28, 28, 16, 28, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588267873 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588267873 Building ZINC001588286632 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588286632 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/446 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001588286632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588286632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588286632 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 25, 25, 22, 25, 25, 7, 15, 15, 15, 15, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 25, 25, 25, 25, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/447 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001588286632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588286632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588286632 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 25, 25, 22, 25, 25, 7, 15, 15, 7, 10, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 25, 25, 25, 25, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588286632 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 Building ZINC001588286632 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588286632 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 446) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001588286632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588286632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588286632 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 25, 25, 22, 25, 25, 7, 15, 15, 15, 15, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 25, 25, 25, 25, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 447) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001588286632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588286632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001588286632 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 18, 25, 25, 22, 25, 25, 7, 15, 15, 7, 10, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 25, 25, 25, 25, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001588286632 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001588286632 Building ZINC001595310905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595310905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/448 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595310905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310905 none CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 13, 13, 21, 21, 21, 21, 21, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 15, 15, 8, 15, 15, 8, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 13, 13, 13, 13, 8, 15, 15, 8, 15, 15, 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]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/449 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595310905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310905 none CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 22, 22, 14, 14, 22, 22, 22, 22, 22, 14, 14, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 14, 14, 8, 14, 14, 7, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 14, 14, 14, 14, 7, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595310905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 Building ZINC001595310905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595310905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 448) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595310905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310905 none CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 13, 13, 21, 21, 21, 21, 21, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 15, 15, 8, 15, 15, 8, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 13, 13, 13, 13, 8, 15, 15, 8, 15, 15, 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]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 449) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595310905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310905 none CC1(C)[C@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 22, 22, 14, 14, 22, 22, 22, 22, 22, 14, 14, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 14, 14, 8, 14, 14, 7, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 14, 14, 14, 14, 7, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595310905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310905 Building ZINC001595310906 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595310906 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/450 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595310906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310906 none CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 19, 19, 17, 17, 19, 19, 19, 19, 19, 15, 15, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 14, 14, 8, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 15, 15, 15, 15, 8, 14, 14, 8, 14, 14, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/451 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595310906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310906 none CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 15, 15, 19, 19, 19, 19, 19, 12, 12, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 16, 16, 10, 16, 16, 8, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 12, 12, 12, 12, 8, 16, 16, 16, 16, 16, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595310906 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 Building ZINC001595310906 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595310906 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 450) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595310906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310906 none CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 19, 19, 17, 17, 19, 19, 19, 19, 19, 15, 15, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 14, 14, 8, 15, 15, 15, 15, 15, 15, 19, 19, 19, 19, 15, 15, 15, 15, 8, 14, 14, 8, 14, 14, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 451) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001595310906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595310906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001595310906 none CC1(C)[C@@H](c2ccc(C(F)(F)F)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 15, 15, 19, 19, 19, 19, 19, 12, 12, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 16, 16, 10, 16, 16, 8, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 12, 12, 12, 12, 8, 16, 16, 16, 16, 16, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595310906 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595310906 Building ZINC001595433931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595433931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/452 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/452' -> `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)Nc1cnc(Br)c2ccccc12) `ZINC001595433931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595433931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001595433931 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12 NO_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', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 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]) total number of confs: 68 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/453 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/453' -> `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)Nc1cnc(Br)c2ccccc12) `ZINC001595433931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595433931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001595433931 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12 NO_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', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 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]) total number of confs: 74 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595433931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 Building ZINC001595433931 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595433931 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 452) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12) `ZINC001595433931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595433931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001595433931 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12 NO_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', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 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]) total number of confs: 68 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 453) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12) `ZINC001595433931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595433931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001595433931 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c2ccccc12 NO_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', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 6, 23, 23, 23, 23, 23] 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]) total number of confs: 74 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595433931 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595433931 Building ZINC001595443023 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595443023 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/454 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=O)OC(C)(C)C) `ZINC001595443023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595443023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001595443023 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=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.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 36, 36, 41, 41, 41, 41, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/455 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=O)OC(C)(C)C) `ZINC001595443023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595443023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001595443023 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=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.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 38, 38, 42, 42, 42, 42, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 12, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595443023 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 Building ZINC001595443023 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595443023 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 454) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=O)OC(C)(C)C) `ZINC001595443023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595443023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001595443023 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=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.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 36, 36, 41, 41, 41, 41, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 455) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=O)OC(C)(C)C) `ZINC001595443023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595443023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001595443023 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cccc1C(=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.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 38, 38, 42, 42, 42, 42, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 12, 12, 12, 12, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595443023 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595443023 Building ZINC001595453577 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595453577 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/456 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1) `ZINC001595453577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595453577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001595453577 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 16, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 16, 16, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 44] set([0, 1, 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, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/457 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1) `ZINC001595453577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595453577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001595453577 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 16, 16, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 44] set([0, 1, 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, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595453577 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 Building ZINC001595453577 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595453577 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 456) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1) `ZINC001595453577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595453577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001595453577 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 16, 16, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 16, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 16, 16, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 44] set([0, 1, 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, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 457) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1) `ZINC001595453577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595453577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001595453577 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(C3CCN(C(=O)OC(C)(C)C)CC3)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 16, 16, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 44] set([0, 1, 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, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595453577 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595453577 Building ZINC001595746345 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595746345 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/458 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001595746345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595746345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001595746345 none O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 16, 16, 34, 34, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/459 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001595746345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595746345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001595746345 none O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 16, 16, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595746345 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 Building ZINC001595746345 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595746345 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 458) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001595746345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595746345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001595746345 none O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 16, 16, 34, 34, 34, 34, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 459) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001595746345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595746345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001595746345 none O=C(NCc1cccnc1Oc1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 16, 16, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595746345 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595746345 Building ZINC001595769303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595769303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/460 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1) `ZINC001595769303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595769303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595769303 none COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 36, 36, 5, 36, 36, 37, 36, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 36, 43, 43, 43, 13, 37, 37, 37, 36, 5, 5, 5, 3, 3, 1, 3, 36] 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, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/461 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1) `ZINC001595769303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595769303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595769303 none COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 5, 27, 27, 34, 27, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 27, 34, 34, 34, 5, 34, 34, 34, 27, 5, 5, 5, 3, 3, 1, 3, 27] 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, 41, 42, 43, 44]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595769303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 Building ZINC001595769303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595769303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 460) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1) `ZINC001595769303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595769303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595769303 none COc1cc(OC)cc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 36, 36, 5, 36, 36, 37, 36, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 36, 43, 43, 43, 13, 37, 37, 37, 36, 5, 5, 5, 3, 3, 1, 3, 36] 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, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 461) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1) `ZINC001595769303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595769303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595769303 none COc1cc(OC)cc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 27, 5, 27, 27, 34, 27, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 27, 34, 34, 34, 5, 34, 34, 34, 27, 5, 5, 5, 3, 3, 1, 3, 27] 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, 41, 42, 43, 44]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595769303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595769303 Building ZINC001595841654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/462 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/463 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/464 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/464' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/465 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/465' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 Building ZINC001595841654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 462) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 463) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 464) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 465) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 Building ZINC001595841654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 462) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 463) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 464) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 465) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 Building ZINC001595841654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 462) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 463) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 5, 4, 2, 4, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 464) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 465) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841654 none C[C@@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 20, 20, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 5, 4, 1, 4, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841654 Building ZINC001595841656 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841656 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/466 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/467 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/468 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/468' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/469 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/469' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841656 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 Building ZINC001595841656 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841656 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 466) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 467) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 468) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 469) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841656 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 Building ZINC001595841656 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841656 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 466) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 467) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 468) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 469) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841656 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 Building ZINC001595841656 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001595841656 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 466) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 467) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 4, 3, 1, 3, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 468) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 469) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl) `ZINC001595841656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001595841656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001595841656 none C[C@H]1COCCN1c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 27, 9, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 4, 3, 1, 3, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595841656 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595841656 Building ZINC001595893778 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595893778 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/470 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl) `ZINC001595893778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595893778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001595893778 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/471 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl) `ZINC001595893778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595893778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001595893778 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595893778 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 Building ZINC001595893778 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595893778 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 470) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl) `ZINC001595893778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595893778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001595893778 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 471) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl) `ZINC001595893778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595893778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001595893778 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595893778 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595893778 Building ZINC001595906908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595906908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/472 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595906908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906908 none O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 3, 3, 12, 20, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 7, 12, 12, 20, 20, 126, 42, 42, 42, 42, 42, 7, 7, 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, 44]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/473 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595906908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906908 none O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 4, 6, 11, 20, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 2, 6, 6, 11, 11, 20, 20, 120, 40, 40, 40, 40, 40, 6, 6, 6, 6] 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, 44]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595906908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 Building ZINC001595906908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595906908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 472) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595906908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906908 none O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 3, 3, 12, 20, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 1, 1, 1, 5, 5, 5, 5, 5, 3, 7, 7, 12, 12, 20, 20, 126, 42, 42, 42, 42, 42, 7, 7, 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, 44]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 473) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595906908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906908 none O=C(Nc1ccc(CC[C@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 4, 6, 11, 20, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 2, 6, 6, 11, 11, 20, 20, 120, 40, 40, 40, 40, 40, 6, 6, 6, 6] 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, 44]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595906908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906908 Building ZINC001595906909 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595906909 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/474 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595906909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906909 none O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 2, 2, 11, 20, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 2, 6, 6, 11, 11, 20, 20, 120, 40, 40, 40, 40, 40, 6, 6, 6, 6] 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, 44]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/475 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595906909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906909 none O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 12, 20, 41, 41, 41, 41, 41, 41, 41, 41, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 3, 7, 7, 12, 12, 20, 20, 123, 41, 41, 41, 41, 41, 7, 7, 6, 6] 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, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595906909 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 Building ZINC001595906909 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595906909 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 474) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595906909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906909 none O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 2, 2, 11, 20, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 2, 6, 6, 11, 11, 20, 20, 120, 40, 40, 40, 40, 40, 6, 6, 6, 6] 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, 44]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 475) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001595906909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595906909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001595906909 none O=C(Nc1ccc(CC[C@@H](O)c2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 12, 20, 41, 41, 41, 41, 41, 41, 41, 41, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 3, 7, 7, 12, 12, 20, 20, 123, 41, 41, 41, 41, 41, 7, 7, 6, 6] 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, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595906909 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595906909 Building ZINC001595908746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595908746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/476 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F) `ZINC001595908746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595908746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908746 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 25, 25, 25, 49, 49, 49, 50, 50, 49, 50, 50, 10, 9, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 25, 49, 49, 49, 50, 50, 49, 50, 50, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/477 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F) `ZINC001595908746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595908746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908746 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 25, 23, 23, 46, 46, 46, 48, 48, 46, 48, 48, 8, 8, 8, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 25, 46, 46, 46, 48, 48, 47, 48, 48, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595908746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 Building ZINC001595908746 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595908746 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 476) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F) `ZINC001595908746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595908746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908746 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 25, 25, 25, 49, 49, 49, 50, 50, 49, 50, 50, 10, 9, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 25, 49, 49, 49, 50, 50, 49, 50, 50, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 477) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F) `ZINC001595908746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595908746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908746 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 25, 23, 23, 46, 46, 46, 48, 48, 46, 48, 48, 8, 8, 8, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 25, 46, 46, 46, 48, 48, 47, 48, 48, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595908746 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908746 Building ZINC001595908747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595908747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/478 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F) `ZINC001595908747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595908747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908747 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/479 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F) `ZINC001595908747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595908747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908747 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 26, 24, 24, 46, 46, 46, 47, 47, 47, 47, 47, 10, 10, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 26, 46, 46, 46, 47, 47, 47, 47, 47, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595908747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 Building ZINC001595908747 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595908747 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 478) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F) `ZINC001595908747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595908747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908747 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 24, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 479) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F) `ZINC001595908747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595908747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001595908747 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c(C(=O)N[C@H](C)c2ccccc2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 26, 24, 24, 46, 46, 46, 47, 47, 47, 47, 47, 10, 10, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 2, 2, 26, 46, 46, 46, 47, 47, 47, 47, 47, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595908747 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595908747 Building ZINC001595916894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595916894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/480 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/480' -> `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)N1CCc2c1cccc2C) `ZINC001595916894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595916894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001595916894 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 3, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 34, 34, 4, 34, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/481 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/481' -> `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)N1CCc2c1cccc2C) `ZINC001595916894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595916894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001595916894 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 3, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 34, 34, 3, 34, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595916894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 Building ZINC001595916894 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001595916894 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 480) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C) `ZINC001595916894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001595916894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001595916894 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 3, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 34, 34, 4, 34, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 481) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C) `ZINC001595916894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001595916894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001595916894 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2c1cccc2C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 3, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 34, 34, 3, 34, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001595916894 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001595916894 Building ZINC001596056147 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596056147 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/482 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl) `ZINC001596056147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596056147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001596056147 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 17, 25, 25, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 25, 31, 31, 31, 25, 25, 6, 3, 4, 4, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/483 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl) `ZINC001596056147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596056147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001596056147 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 17, 25, 25, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 25, 31, 31, 31, 25, 25, 6, 3, 4, 4, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596056147 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 Building ZINC001596056147 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596056147 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 482) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl) `ZINC001596056147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596056147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001596056147 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 17, 25, 25, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 25, 31, 31, 31, 25, 25, 6, 3, 4, 4, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 483) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl) `ZINC001596056147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596056147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001596056147 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 25, 17, 25, 25, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 25, 31, 31, 31, 25, 25, 6, 3, 4, 4, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596056147 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596056147 Building ZINC001596166045 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596166045 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/484 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001596166045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596166045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596166045 none O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', '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.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 33, 33, 33, 33, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/485 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001596166045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596166045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596166045 none O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', '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.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 33, 33, 33, 33, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596166045 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 Building ZINC001596166045 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596166045 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 484) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001596166045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596166045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596166045 none O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', '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.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 33, 33, 33, 33, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 485) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001596166045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596166045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596166045 none O=C(N1CC=C(c2c[nH]c3cc(F)ccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', '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.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 33, 33, 33, 33, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596166045 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596166045 Building ZINC001596171411 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596171411 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/486 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001596171411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596171411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001596171411 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 16, 9, 16, 35, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 2] 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/487 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001596171411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596171411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001596171411 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 10, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 2, 1, 2] 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596171411 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 Building ZINC001596171411 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596171411 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 486) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001596171411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596171411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001596171411 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 16, 9, 16, 35, 35, 35, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 2, 1, 2] 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 487) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001596171411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596171411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001596171411 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 10, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 2, 1, 2] 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596171411 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596171411 Building ZINC001596202207 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596202207 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/488 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1) `ZINC001596202207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596202207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001596202207 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 32, 32, 19, 10, 32, 32, 32, 10, 10, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/489 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1) `ZINC001596202207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596202207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001596202207 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 31, 31, 19, 19, 31, 31, 31, 10, 10, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 10, 10, 10, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596202207 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 Building ZINC001596202207 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596202207 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 488) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1) `ZINC001596202207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596202207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001596202207 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 32, 32, 19, 10, 32, 32, 32, 10, 10, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 10, 10, 10, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 489) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1) `ZINC001596202207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596202207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001596202207 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(Cl)cc2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 31, 31, 19, 19, 31, 31, 31, 10, 10, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 10, 10, 10, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596202207 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596202207 Building ZINC001596330901 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596330901 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/490 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21) `ZINC001596330901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596330901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001596330901 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 39, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 39, 39, 39, 17, 17, 4, 3, 1, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/491 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21) `ZINC001596330901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596330901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001596330901 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 33, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 16, 16, 3, 3, 1, 3, 12, 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]) total number of confs: 140 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596330901 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 Building ZINC001596330901 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596330901 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 490) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21) `ZINC001596330901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596330901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001596330901 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 39, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 39, 39, 39, 17, 17, 4, 3, 1, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 491) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21) `ZINC001596330901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596330901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001596330901 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 33, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 16, 16, 3, 3, 1, 3, 12, 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]) total number of confs: 140 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596330901 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596330901 Building ZINC001596355552 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596355552 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/492 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl) `ZINC001596355552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596355552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596355552 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 21, 21, 15, 21, 21, 21, 21, 21, 21, 8, 6, 6, 6, 17, 17, 17, 6, 6, 4, 21, 21, 21, 21, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/493 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl) `ZINC001596355552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596355552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596355552 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 21, 21, 8, 16, 21, 21, 21, 21, 21, 8, 8, 8, 8, 19, 19, 19, 8, 8, 4, 21, 21, 21, 21, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596355552 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 Building ZINC001596355552 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596355552 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 492) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl) `ZINC001596355552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596355552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596355552 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 21, 21, 15, 21, 21, 21, 21, 21, 21, 8, 6, 6, 6, 17, 17, 17, 6, 6, 4, 21, 21, 21, 21, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 493) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl) `ZINC001596355552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596355552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596355552 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nnc(c3ccc(C(F)(F)F)cc3)s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 21, 21, 8, 16, 21, 21, 21, 21, 21, 8, 8, 8, 8, 19, 19, 19, 8, 8, 4, 21, 21, 21, 21, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596355552 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596355552 Building ZINC001596423248 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596423248 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/494 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1) `ZINC001596423248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596423248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596423248 none Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 23, 23, 23, 23, 23, 23, 23, 22, 31, 31, 31, 31, 31, 15, 15, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/495 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1) `ZINC001596423248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596423248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596423248 none Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 31, 31, 31, 31, 31, 15, 15, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596423248 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 Building ZINC001596423248 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596423248 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 494) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1) `ZINC001596423248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596423248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596423248 none Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 23, 23, 23, 23, 23, 23, 23, 22, 31, 31, 31, 31, 31, 15, 15, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 495) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1) `ZINC001596423248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596423248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596423248 none Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 31, 31, 31, 31, 31, 15, 15, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596423248 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596423248 Building ZINC001596424863 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596424863 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/496 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1) `ZINC001596424863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596424863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/497 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1) `ZINC001596424863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596424863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 3, 3, 3, 21, 21, 4, 21, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596424863 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 Building ZINC001596424863 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596424863 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 496) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1) `ZINC001596424863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596424863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 3, 3, 3, 25, 25, 3, 25, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 497) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1) `ZINC001596424863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596424863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424863 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 4, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 3, 3, 3, 21, 21, 4, 21, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596424863 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424863 Building ZINC001596424864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596424864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/498 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1) `ZINC001596424864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596424864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 3, 3, 3, 20, 20, 20, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 43 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/499 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1) `ZINC001596424864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596424864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 3, 3, 3, 25, 25, 4, 25, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596424864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 Building ZINC001596424864 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596424864 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 498) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1) `ZINC001596424864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596424864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 3, 3, 3, 20, 20, 20, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 43 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 499) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1) `ZINC001596424864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596424864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596424864 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C)(C)[C@H]1c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 25, 25, 3, 25, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 3, 3, 3, 25, 25, 4, 25, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596424864 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596424864 Building ZINC001596446498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596446498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/500 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596446498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446498 none COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 3, 8, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 5, 6, 6, 6, 25, 25, 25, 16, 16, 8, 8, 8, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/501 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596446498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446498 none COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 5, 8, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 5, 7, 7, 7, 6, 7, 7, 7, 33, 33, 33, 21, 21, 8, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596446498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 Building ZINC001596446498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596446498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 500) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596446498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446498 none COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 3, 8, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 5, 6, 6, 6, 25, 25, 25, 16, 16, 8, 8, 8, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 501) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596446498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446498 none COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 5, 8, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 5, 7, 7, 7, 6, 7, 7, 7, 33, 33, 33, 21, 21, 8, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596446498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446498 Building ZINC001596446499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596446499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/502 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596446499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446499 none COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 4, 8, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 4, 6, 6, 6, 5, 6, 6, 6, 33, 33, 33, 21, 21, 8, 8, 8, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/503 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596446499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446499 none COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 6, 3, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 3, 5, 5, 5, 4, 5, 5, 5, 24, 24, 24, 14, 14, 6, 6, 6, 4, 4, 4, 12, 12, 5, 12, 12, 4, 4, 4, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596446499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 Building ZINC001596446499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596446499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 502) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596446499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446499 none COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 4, 8, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 4, 6, 6, 6, 5, 6, 6, 6, 33, 33, 33, 21, 21, 8, 8, 8, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 503) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C) `ZINC001596446499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596446499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001596446499 none COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 6, 3, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 3, 5, 5, 5, 4, 5, 5, 5, 24, 24, 24, 14, 14, 6, 6, 6, 4, 4, 4, 12, 12, 5, 12, 12, 4, 4, 4, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596446499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596446499 Building ZINC001596469790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596469790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/504 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001596469790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596469790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001596469790 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 21, 11, 11, 11, 11, 11, 11, 11, 7, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 28, 28, 28, 28, 28, 23, 23, 23, 23, 11, 11, 11, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/505 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001596469790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596469790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001596469790 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 22, 24, 24, 22, 12, 12, 12, 7, 12, 12, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 6, 2, 30, 30, 30, 30, 30, 24, 22, 24, 24, 12, 12, 12, 7, 7, 3, 3, 3, 2, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596469790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 Building ZINC001596469790 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596469790 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 504) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001596469790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596469790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001596469790 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 21, 11, 11, 11, 11, 11, 11, 11, 7, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 28, 28, 28, 28, 28, 23, 23, 23, 23, 11, 11, 11, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 505) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC001596469790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596469790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001596469790 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 22, 24, 24, 22, 12, 12, 12, 7, 12, 12, 12, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 6, 2, 30, 30, 30, 30, 30, 24, 22, 24, 24, 12, 12, 12, 7, 7, 3, 3, 3, 2, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596469790 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596469790 Building ZINC001596486294 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596486294 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/506 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001596486294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596486294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596486294 none O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [16, 1, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/507 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001596486294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596486294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596486294 none O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [15, 1, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596486294 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 Building ZINC001596486294 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596486294 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 506) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001596486294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596486294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596486294 none O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [16, 1, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 507) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001596486294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596486294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001596486294 none O=C(N1Cc2cc(Br)ccc2OC2(CCC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [15, 1, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596486294 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596486294 Building ZINC001596537835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596537835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/508 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)cc2)cn1) `ZINC001596537835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596537835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001596537835 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 28, 28, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 6, 6, 18, 28, 28, 28, 28, 28, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/509 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)cc2)cn1) `ZINC001596537835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596537835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001596537835 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 28, 28, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 6, 6, 19, 28, 28, 28, 28, 28, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596537835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 Building ZINC001596537835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596537835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 508) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)cc2)cn1) `ZINC001596537835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596537835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001596537835 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 28, 28, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 6, 6, 18, 28, 28, 28, 28, 28, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 509) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)cc2)cn1) `ZINC001596537835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596537835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001596537835 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3nc(C(F)(F)F)cc3C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 3, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 28, 28, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 6, 6, 19, 28, 28, 28, 28, 28, 6, 6, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596537835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596537835 Building ZINC001596597398 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596597398 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/510 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001596597398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596597398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001596597398 none CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['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', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 3, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/511 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001596597398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596597398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001596597398 none CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['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', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 3, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596597398 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 Building ZINC001596597398 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596597398 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 510) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001596597398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596597398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001596597398 none CC(C)Oc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['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', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 3, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 511) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br) `ZINC001596597398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596597398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001596597398 none CC(C)Oc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1Br NO_LONG_NAME dock atom types: ['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', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 13, 3, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596597398 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596597398 Building ZINC001596599468 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596599468 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/512 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/512' -> `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)N1CCCc2c(Cl)cc(Cl)cc21) `ZINC001596599468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596599468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001596599468 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 1, 1, 1, 3, 11, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 83 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/513 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/513' -> `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)N1CCCc2c(Cl)cc(Cl)cc21) `ZINC001596599468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596599468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001596599468 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 1, 1, 1, 3, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 84 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596599468 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 Building ZINC001596599468 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596599468 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 512) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21) `ZINC001596599468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596599468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001596599468 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 1, 1, 1, 3, 11, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 83 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 513) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21) `ZINC001596599468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596599468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001596599468 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c(Cl)cc(Cl)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 1, 1, 1, 3, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 84 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596599468 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596599468 Building ZINC001596678304 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596678304 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/514 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/514' -> `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)Nc1nc2c(s1)c(Cl)ccc2F) `ZINC001596678304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596678304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001596678304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 5, 16, 16, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 5, 9, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/515 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/515' -> `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)Nc1nc2c(s1)c(Cl)ccc2F) `ZINC001596678304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596678304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001596678304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 6, 15, 15, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 15, 15, 10, 15, 15, 5, 5, 5, 9, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596678304 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 Building ZINC001596678304 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596678304 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 514) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F) `ZINC001596678304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596678304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001596678304 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 5, 16, 16, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 5, 9, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 515) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F) `ZINC001596678304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596678304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001596678304 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2c(s1)c(Cl)ccc2F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 6, 15, 15, 5, 5, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 15, 15, 10, 15, 15, 5, 5, 5, 9, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 80 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596678304 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596678304 Building ZINC001596794454 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596794454 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/516 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/516' -> `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(C)cc(NC(=O)OC(C)(C)C)c1) `ZINC001596794454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596794454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001596794454 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 30, 40, 40, 42, 42, 42, 42, 7, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 7, 7, 7, 7, 7, 30, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 56, 57, 58, 59, 60]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/517 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/517' -> `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(C)cc(NC(=O)OC(C)(C)C)c1) `ZINC001596794454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596794454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001596794454 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 27, 36, 36, 39, 39, 39, 39, 7, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 7, 7, 7, 7, 7, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596794454 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 Building ZINC001596794454 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596794454 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 516) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1) `ZINC001596794454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596794454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001596794454 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 30, 40, 40, 42, 42, 42, 42, 7, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 7, 7, 7, 7, 7, 30, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 56, 57, 58, 59, 60]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 517) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1) `ZINC001596794454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596794454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001596794454 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)cc(NC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 27, 36, 36, 39, 39, 39, 39, 7, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 7, 7, 7, 7, 7, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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, 56, 57, 58, 59, 60]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596794454 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596794454 Building ZINC001596874885 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596874885 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/518 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/518' -> `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)Nc1ncsc1C1CC1) `ZINC001596874885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596874885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596874885 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1 NO_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.2', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 14, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 9, 9, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/519 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/519' -> `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)Nc1ncsc1C1CC1) `ZINC001596874885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596874885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596874885 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1 NO_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.2', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 14, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 13, 13, 4, 4, 4, 23, 23, 7, 23, 4, 4, 4, 5, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596874885 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 Building ZINC001596874885 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596874885 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 518) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1) `ZINC001596874885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596874885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596874885 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1 NO_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.2', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 14, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 9, 9, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 519) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1) `ZINC001596874885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596874885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001596874885 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncsc1C1CC1 NO_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.2', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 14, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 13, 13, 4, 4, 4, 23, 23, 7, 23, 4, 4, 4, 5, 9, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596874885 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596874885 Building ZINC001596909228 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596909228 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/520 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001596909228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596909228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596909228 none Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 7, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 7, 7, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 60 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/521 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001596909228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596909228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596909228 none Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 7, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 7, 7, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596909228 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 Building ZINC001596909228 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596909228 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 520) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001596909228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596909228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596909228 none Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 7, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 7, 7, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 60 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 521) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001596909228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596909228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001596909228 none Cc1[nH]c2ccccc2c1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 7, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 7, 7, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001596909228 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001596909228 Building ZINC001597026966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597026966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/522 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/522' -> `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)Nc1ccnc(Cl)c1F) `ZINC001597026966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597026966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001597026966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/523 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/523' -> `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)Nc1ccnc(Cl)c1F) `ZINC001597026966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597026966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001597026966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597026966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 Building ZINC001597026966 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597026966 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 522) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F) `ZINC001597026966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597026966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001597026966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 523) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F) `ZINC001597026966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597026966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001597026966 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597026966 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597026966 Building ZINC001597212636 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597212636 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/524 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C) `ZINC001597212636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597212636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597212636 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 3, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/525 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C) `ZINC001597212636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597212636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597212636 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 3, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597212636 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 Building ZINC001597212636 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597212636 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 524) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C) `ZINC001597212636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597212636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597212636 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 3, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 525) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C) `ZINC001597212636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597212636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597212636 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 3, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597212636 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597212636 Building ZINC001597341800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597341800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/526 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/526' -> `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)Nc1noc(C(C)(C)C)c1C) `ZINC001597341800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597341800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597341800 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C NO_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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 23, 23, 5, 23, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/527 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/527' -> `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)Nc1noc(C(C)(C)C)c1C) `ZINC001597341800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597341800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597341800 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C NO_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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597341800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 Building ZINC001597341800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597341800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 526) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C) `ZINC001597341800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597341800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597341800 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C NO_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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 23, 23, 5, 23, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 527) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C) `ZINC001597341800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597341800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001597341800 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1noc(C(C)(C)C)c1C NO_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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 12, 1, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 23, 23, 4, 23, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597341800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597341800 Building ZINC001597376618 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597376618 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/528 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1) `ZINC001597376618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597376618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001597376618 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 11, 3, 2, 2, 4, 2, 2, 11, 23, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/529 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1) `ZINC001597376618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597376618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001597376618 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 24, 24, 50, 50, 40, 50, 50, 50, 50, 50, 50, 24, 12, 12, 12, 3, 2, 2, 4, 2, 2, 12, 24, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597376618 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 Building ZINC001597376618 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597376618 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 528) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1) `ZINC001597376618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597376618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001597376618 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 11, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 11, 3, 2, 2, 4, 2, 2, 11, 23, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 529) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1) `ZINC001597376618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597376618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001597376618 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c1)Nc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 24, 24, 50, 50, 40, 50, 50, 50, 50, 50, 50, 24, 12, 12, 12, 3, 2, 2, 4, 2, 2, 12, 24, 50, 50, 50, 50] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597376618 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597376618 Building ZINC001597396091 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597396091 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/530 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/530' -> `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@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597396091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396091 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 42, 42, 42, 42, 42, 42, 14, 20, 20, 14, 20, 20, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 14, 14, 14, 42, 42, 42, 42, 42, 42, 42, 20, 20, 14, 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, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 217 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/531 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/531' -> `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@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597396091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396091 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 41, 41, 41, 41, 41, 41, 13, 22, 22, 13, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 22, 22, 13, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 216 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597396091 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 Building ZINC001597396091 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597396091 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 530) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597396091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396091 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 42, 42, 42, 42, 42, 42, 14, 20, 20, 14, 20, 20, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 14, 14, 14, 42, 42, 42, 42, 42, 42, 42, 20, 20, 14, 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, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 217 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 531) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597396091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396091 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 41, 41, 41, 41, 41, 41, 13, 22, 22, 13, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 22, 22, 13, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 216 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597396091 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396091 Building ZINC001597396092 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597396092 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/532 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/532' -> `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@@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597396092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396092 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 44, 44, 44, 44, 44, 44, 13, 22, 22, 13, 22, 22, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 13, 13, 13, 44, 44, 44, 44, 44, 44, 44, 22, 22, 13, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/533 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/533' -> `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@@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597396092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396092 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 42, 42, 42, 42, 42, 42, 14, 20, 20, 14, 20, 20, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 14, 14, 14, 42, 42, 42, 42, 42, 42, 42, 20, 20, 14, 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, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 211 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597396092 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 Building ZINC001597396092 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597396092 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 532) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597396092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396092 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 44, 44, 44, 44, 44, 44, 13, 22, 22, 13, 22, 22, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 13, 13, 13, 44, 44, 44, 44, 44, 44, 44, 22, 22, 13, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 533) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1) `ZINC001597396092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597396092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001597396092 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@](C)(Cc1ccccc1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 14, 14, 42, 42, 42, 42, 42, 42, 14, 20, 20, 14, 20, 20, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 14, 14, 14, 42, 42, 42, 42, 42, 42, 42, 20, 20, 14, 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, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 211 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597396092 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597396092 Building ZINC001597436301 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597436301 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/534 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001597436301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597436301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001597436301 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 27, 27, 27, 21, 21, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 21, 21, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/535 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001597436301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597436301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001597436301 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 27, 27, 27, 24, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 21, 21, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597436301 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 Building ZINC001597436301 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597436301 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 534) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001597436301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597436301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001597436301 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 27, 27, 27, 21, 21, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 21, 21, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 535) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001597436301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597436301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001597436301 none O=C(NCc1c(Cl)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 16, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 27, 27, 27, 24, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 21, 21, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597436301 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597436301 Building ZINC001597485088 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597485088 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/536 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl) `ZINC001597485088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597485088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001597485088 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 28, 28, 18, 19, 28, 28, 17, 17, 17, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 28, 28, 28, 28, 17, 17, 17, 2] 50 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/537 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl) `ZINC001597485088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597485088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001597485088 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 26, 26, 15, 21, 26, 26, 15, 15, 15, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 26, 26, 26, 26, 15, 15, 15, 2] 50 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597485088 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 Building ZINC001597485088 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597485088 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 536) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl) `ZINC001597485088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597485088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001597485088 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 28, 28, 18, 19, 28, 28, 17, 17, 17, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 28, 28, 28, 28, 17, 17, 17, 2] 50 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 537) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl) `ZINC001597485088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597485088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001597485088 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc(c3ccc(Cl)cc3)c(C)s2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 5, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 26, 26, 15, 21, 26, 26, 15, 15, 15, 2, 2, 2, 4, 4, 4, 2, 2, 1, 6, 6, 26, 26, 26, 26, 15, 15, 15, 2] 50 rigid atoms, others: [33, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597485088 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597485088 Building ZINC001597511649 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597511649 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/538 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001597511649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597511649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001597511649 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 37, 50, 50, 40, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 37, 37, 50, 50, 50, 50, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/539 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001597511649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597511649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001597511649 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 36, 50, 50, 39, 39, 50, 50, 50, 50, 50, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 36, 36, 50, 50, 50, 50, 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597511649 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 Building ZINC001597511649 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597511649 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 538) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001597511649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597511649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001597511649 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 37, 50, 50, 40, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 37, 37, 50, 50, 50, 50, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 539) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001597511649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597511649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001597511649 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 36, 50, 50, 39, 39, 50, 50, 50, 50, 50, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 36, 36, 50, 50, 50, 50, 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]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597511649 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597511649 Building ZINC001597636141 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597636141 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/540 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21) `ZINC001597636141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597636141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001597636141 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 14, 17, 17, 20, 20, 19, 19, 20, 20, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 20, 20, 20, 20, 17, 17, 17] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/541 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21) `ZINC001597636141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597636141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001597636141 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 15, 18, 18, 20, 20, 18, 18, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 20, 20, 20, 20, 18, 18, 18] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597636141 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 Building ZINC001597636141 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597636141 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 540) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21) `ZINC001597636141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597636141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001597636141 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 14, 17, 17, 20, 20, 19, 19, 20, 20, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 20, 20, 20, 20, 17, 17, 17] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 541) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21) `ZINC001597636141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597636141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001597636141 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1c(c2ccc(F)cc2)nc2ccc(C(F)(F)F)cn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 15, 18, 18, 20, 20, 18, 18, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 20, 20, 20, 20, 18, 18, 18] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597636141 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597636141 Building ZINC001597687301 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597687301 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/542 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001597687301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597687301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001597687301 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 4, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/543 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001597687301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597687301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001597687301 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 4, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597687301 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 Building ZINC001597687301 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597687301 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 542) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001597687301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597687301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001597687301 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 4, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 4, 4, 4, 17, 17, 8, 17, 4, 4, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 543) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1) `ZINC001597687301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597687301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001597687301 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 6, 6, 3, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 6, 4, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001597687301 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001597687301 Building ZINC001598030384 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598030384 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/544 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598030384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030384 none O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 14, 14, 9, 14, 14, 14, 26, 29, 29, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 14, 14, 14, 14, 29, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/545 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598030384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030384 none O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 15, 15, 10, 15, 15, 15, 26, 28, 28, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 28, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598030384 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 Building ZINC001598030384 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598030384 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 544) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598030384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030384 none O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 14, 14, 9, 14, 14, 14, 26, 29, 29, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 14, 14, 14, 14, 29, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 545) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598030384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030384 none O=C(N[C@@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 15, 15, 10, 15, 15, 15, 26, 28, 28, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 28, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598030384 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030384 Building ZINC001598030386 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598030386 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/546 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598030386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030386 none O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 13, 13, 9, 13, 13, 13, 25, 30, 30, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 13, 13, 13, 30, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/547 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598030386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030386 none O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 15, 15, 10, 15, 15, 15, 26, 29, 29, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 29, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598030386 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 Building ZINC001598030386 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598030386 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 546) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598030386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030386 none O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 13, 13, 9, 13, 13, 13, 25, 30, 30, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 13, 13, 13, 30, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 547) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001598030386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598030386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001598030386 none O=C(N[C@H](c1ccccc1OC(F)F)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 15, 15, 10, 15, 15, 15, 26, 29, 29, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 15, 15, 15, 15, 29, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598030386 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598030386 Building ZINC001598053722 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598053722 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/548 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001598053722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598053722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001598053722 none COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 42, 42, 28, 13, 13, 6, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 28, 28, 13, 13, 3, 6, 6, 3, 4, 4, 4, 4, 6, 42, 42] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/549 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001598053722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598053722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001598053722 none COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 35, 25, 12, 12, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 35, 35, 35, 25, 25, 12, 12, 2, 4, 4, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598053722 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 Building ZINC001598053722 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598053722 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 548) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001598053722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598053722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001598053722 none COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 42, 42, 28, 13, 13, 6, 6, 3, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 42, 42, 42, 42, 42, 42, 42, 28, 28, 13, 13, 3, 6, 6, 3, 4, 4, 4, 4, 6, 42, 42] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 549) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001598053722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598053722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001598053722 none COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 35, 35, 25, 12, 12, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 35, 35, 35, 35, 35, 35, 35, 25, 25, 12, 12, 2, 4, 4, 2, 2, 2, 2, 2, 4, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598053722 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598053722 Building ZINC001598140443 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598140443 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/550 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1) `ZINC001598140443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598140443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001598140443 none COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 18, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 18, 18, 5, 5, 2, 4, 4, 7, 7, 7, 4, 5, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/551 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1) `ZINC001598140443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598140443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001598140443 none COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 7, 4, 4, 4, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 2, 4, 4, 7, 7, 7, 4, 5, 31, 31] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598140443 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 Building ZINC001598140443 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598140443 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 550) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1) `ZINC001598140443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598140443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001598140443 none COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 18, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 18, 18, 5, 5, 2, 4, 4, 7, 7, 7, 4, 5, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 551) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1) `ZINC001598140443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598140443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001598140443 none COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(OC)c(Cl)c4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 18, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 7, 4, 4, 4, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 2, 4, 4, 7, 7, 7, 4, 5, 31, 31] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598140443 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598140443 Building ZINC001598190060 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598190060 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/552 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001598190060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598190060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001598190060 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 34, 34, 33, 18, 18, 18, 10, 18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 33, 34, 34, 18, 18, 18, 10, 10, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/553 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001598190060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598190060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001598190060 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 35, 18, 18, 18, 12, 18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 10, 10, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598190060 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 Building ZINC001598190060 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598190060 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 552) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001598190060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598190060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001598190060 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 34, 34, 33, 18, 18, 18, 10, 18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 33, 34, 34, 18, 18, 18, 10, 10, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 553) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001598190060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598190060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001598190060 none CCc1ccccc1Oc1ccc(Cl)cc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 35, 18, 18, 18, 12, 18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 10, 10, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598190060 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598190060 Building ZINC001598230029 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598230029 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/554 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(Br)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2) `ZINC001598230029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598230029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001598230029 none CCc1cc(Br)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6] 25 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/555 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(Br)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2) `ZINC001598230029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598230029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001598230029 none CCc1cc(Br)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6] 25 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598230029 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 Building ZINC001598230029 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598230029 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 554) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1cc(Br)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2) `ZINC001598230029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598230029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001598230029 none CCc1cc(Br)cc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6] 25 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 555) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1cc(Br)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2) `ZINC001598230029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598230029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001598230029 none CCc1cc(Br)cc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6] 25 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598230029 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598230029 Building ZINC001598324815 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598324815 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/556 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598324815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324815 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/557 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598324815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324815 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 10, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598324815 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 Building ZINC001598324815 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598324815 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 556) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598324815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324815 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 557) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598324815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324815 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 10, 10, 10, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598324815 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324815 Building ZINC001598324816 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598324816 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/558 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598324816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324816 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/559 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598324816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324816 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598324816 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 Building ZINC001598324816 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598324816 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 558) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598324816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324816 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 559) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl) `ZINC001598324816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598324816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001598324816 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2cc(F)c(F)c(F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 6, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 12, 12, 12, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598324816 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598324816 Building ZINC001598341063 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598341063 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/560 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598341063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341063 none C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 8, 2, 11, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/561 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598341063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341063 none C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 7, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598341063 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 Building ZINC001598341063 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598341063 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 560) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598341063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341063 none C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 8, 2, 11, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 561) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598341063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341063 none C[C@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 7, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598341063 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341063 Building ZINC001598341064 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598341064 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/562 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598341064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341064 none C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 7, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/563 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598341064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341064 none C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 7, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598341064 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 Building ZINC001598341064 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598341064 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 562) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598341064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341064 none C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 7, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 8, 8] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 563) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001598341064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598341064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001598341064 none C[C@@]1(Cc2cc(F)c(F)c(F)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 7, 2, 10, 1, 1, 1, 9, 9, 9, 9, 9, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598341064 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598341064 Building ZINC001598355330 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001598355330 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/564 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 36, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 36, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/565 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 32, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 32, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/566 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/566' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/567 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/567' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598355330 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 Building ZINC001598355330 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001598355330 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 564) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 36, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 36, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 565) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 32, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 32, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 566) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 567) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598355330 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 Building ZINC001598355330 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001598355330 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 564) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 36, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 36, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 565) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 32, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 32, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 566) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 567) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598355330 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 Building ZINC001598355330 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001598355330 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 564) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 36, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 36, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 565) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 32, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 32, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 566) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 567) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)c2)cn1) `ZINC001598355330.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001598355330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001598355330 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cccc([C@H]3CC[N@@](Cc4ccccc4)CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 9, 14, 14, 14, 14, 14, 28, 36, 36, 28, 36, 36, 14, 14, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 8, 8, 8, 14, 14, 14, 14, 28, 28, 36, 36, 28, 36, 36, 14, 14, 14, 14, 8, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598355330 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598355330 Building ZINC001598404622 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598404622 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/568 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F) `ZINC001598404622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598404622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001598404622 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 22, 25, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/569 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F) `ZINC001598404622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598404622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001598404622 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598404622 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 Building ZINC001598404622 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598404622 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 568) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F) `ZINC001598404622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598404622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001598404622 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 25, 22, 25, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 569) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F) `ZINC001598404622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598404622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001598404622 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598404622 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598404622 Building ZINC001598405783 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598405783 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/570 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F) `ZINC001598405783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598405783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001598405783 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 3, 2, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/571 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F) `ZINC001598405783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598405783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001598405783 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 32, 43, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 3, 2, 2, 2, 2] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598405783 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 Building ZINC001598405783 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598405783 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 570) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F) `ZINC001598405783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598405783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001598405783 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 3, 2, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 571) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F) `ZINC001598405783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598405783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001598405783 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 32, 43, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 3, 2, 2, 2, 2] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598405783 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598405783 Building ZINC001598418596 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598418596 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/572 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1) `ZINC001598418596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598418596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001598418596 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 42, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/573 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1) `ZINC001598418596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598418596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001598418596 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 41, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 25, 34, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598418596 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 Building ZINC001598418596 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598418596 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 572) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1) `ZINC001598418596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598418596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001598418596 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 42, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 573) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1) `ZINC001598418596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598418596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001598418596 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cc(F)ccc1Oc1ccc(F)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 41, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 25, 34, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598418596 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598418596 Building ZINC001598422368 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598422368 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/574 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001598422368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598422368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001598422368 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 23, 26, 26, 26, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 26, 26, 8, 4, 4, 4, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/575 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001598422368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598422368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001598422368 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 23, 26, 26, 26, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 26, 26, 8, 4, 4, 4, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598422368 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 Building ZINC001598422368 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598422368 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 574) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001598422368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598422368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001598422368 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 23, 26, 26, 26, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 26, 26, 8, 4, 4, 4, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 575) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001598422368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598422368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001598422368 none O=C(Nc1ccc(Oc2ccc(Cl)nn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 8, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 23, 26, 26, 26, 26, 26, 26, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 26, 26, 8, 4, 4, 4, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598422368 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598422368 Building ZINC001598436148 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598436148 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/576 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)CC1) `ZINC001598436148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598436148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001598436148 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 10, 1, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 1, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/577 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)CC1) `ZINC001598436148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598436148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001598436148 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 32, 12, 32, 12, 12, 12, 10, 2, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 12, 3, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598436148 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 Building ZINC001598436148 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598436148 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 576) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)CC1) `ZINC001598436148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598436148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001598436148 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 14, 34, 14, 14, 14, 10, 1, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 1, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 577) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)CC1) `ZINC001598436148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598436148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001598436148 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2(CCC2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 32, 12, 32, 12, 12, 12, 10, 2, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49, 12, 12, 12, 12, 3, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598436148 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436148 Building ZINC001598436812 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598436812 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/578 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001598436812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598436812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001598436812 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 8, 16, 25, 37, 37, 50, 50, 50, 50, 8, 8, 8, 8, 8, 3, 3, 3, 2, 1, 2, 16, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/579 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001598436812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598436812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001598436812 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 10, 18, 25, 36, 36, 50, 50, 50, 50, 10, 10, 10, 10, 10, 4, 4, 4, 2, 1, 2, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598436812 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 Building ZINC001598436812 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598436812 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 578) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001598436812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598436812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001598436812 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 8, 16, 25, 37, 37, 50, 50, 50, 50, 8, 8, 8, 8, 8, 3, 3, 3, 2, 1, 2, 16, 16, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 579) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001598436812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598436812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001598436812 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 10, 18, 25, 36, 36, 50, 50, 50, 50, 10, 10, 10, 10, 10, 4, 4, 4, 2, 1, 2, 18, 18, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 168 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598436812 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598436812 Building ZINC001598458309 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598458309 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/580 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1) `ZINC001598458309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598458309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001598458309 none CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 19, 13, 13, 13, 13, 13, 13, 13, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 27, 27, 36, 36, 36, 27, 27, 13, 7, 13, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/581 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1) `ZINC001598458309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598458309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001598458309 none CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 18, 14, 14, 14, 14, 14, 14, 14, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 26, 26, 35, 35, 35, 26, 26, 14, 8, 14, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598458309 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 Building ZINC001598458309 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598458309 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 580) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1) `ZINC001598458309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598458309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001598458309 none CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 19, 13, 13, 13, 13, 13, 13, 13, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 27, 27, 36, 36, 36, 27, 27, 13, 7, 13, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 581) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1) `ZINC001598458309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598458309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001598458309 none CSc1ccc(Oc2ccc(F)cc2CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 18, 14, 14, 14, 14, 14, 14, 14, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 26, 26, 35, 35, 35, 26, 26, 14, 8, 14, 7, 7, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001598458309 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001598458309 Building ZINC001602677617 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001602677617 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/582 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001602677617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001602677617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001602677617 none O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 17, 17, 17, 44, 49, 49, 49, 49, 49, 49, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 44, 44, 49, 49, 49, 49, 17, 17, 3, 2, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/583 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001602677617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001602677617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001602677617 none O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 19, 19, 19, 45, 50, 50, 45, 48, 50, 50, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 19, 45, 45, 50, 50, 50, 50, 19, 19, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001602677617 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 Building ZINC001602677617 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001602677617 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 582) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001602677617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001602677617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001602677617 none O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 17, 17, 17, 44, 49, 49, 49, 49, 49, 49, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 44, 44, 49, 49, 49, 49, 17, 17, 3, 2, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 583) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001602677617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001602677617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001602677617 none O=C(N1CC(Cc2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 19, 19, 19, 45, 50, 50, 45, 48, 50, 50, 19, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 19, 45, 45, 50, 50, 50, 50, 19, 19, 3, 1, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001602677617 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001602677617 Building ZINC001608584587 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001608584587 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/584 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001608584587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001608584587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001608584587 none O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 11, 16, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/585 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001608584587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001608584587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001608584587 none O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 6, 11, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001608584587 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 Building ZINC001608584587 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001608584587 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 584) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001608584587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001608584587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001608584587 none O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 11, 16, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 585) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001608584587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001608584587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001608584587 none O=C(Nc1ccc(Cl)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 6, 11, 16, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 2, 2, 1, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001608584587 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001608584587 Building ZINC001610897177 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610897177 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/586 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl) `ZINC001610897177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610897177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610897177 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 3, 3, 3, 3, 3, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/587 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl) `ZINC001610897177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610897177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610897177 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 3, 3, 3, 3, 3, 16, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610897177 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 Building ZINC001610897177 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610897177 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 586) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl) `ZINC001610897177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610897177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610897177 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 3, 3, 3, 3, 3, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 32, 32, 32, 32, 32, 32, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 587) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl) `ZINC001610897177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610897177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610897177 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(Oc2ccc(F)c(C)c2)cc1Cl 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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 3, 3, 3, 3, 3, 16, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 3] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610897177 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610897177 Building ZINC001610902806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610902806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/588 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001610902806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610902806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001610902806 none CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 6, 9, 9, 9, 9, 9, 9, 9, 24, 31, 31, 26, 31, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 9, 6, 9, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/589 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001610902806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610902806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001610902806 none CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 6, 9, 9, 9, 9, 9, 9, 9, 24, 31, 31, 24, 29, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 9, 7, 9, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610902806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 Building ZINC001610902806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610902806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 588) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001610902806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610902806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001610902806 none CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 6, 9, 9, 9, 9, 9, 9, 9, 24, 31, 31, 26, 31, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 9, 6, 9, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 589) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001610902806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610902806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001610902806 none CCN(Cc1cc(F)ccc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 6, 9, 9, 9, 9, 9, 9, 9, 24, 31, 31, 24, 29, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 9, 7, 9, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610902806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610902806 Building ZINC001610919887 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610919887 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/590 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1) `ZINC001610919887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610919887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001610919887 none CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 26, 30, 30, 26, 6, 4, 6, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 6, 6, 6, 37, 37, 37, 37, 37, 30, 26, 30, 30, 6, 6, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 6] 50 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/591 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1) `ZINC001610919887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610919887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001610919887 none CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 26, 30, 30, 26, 6, 5, 6, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 6, 6, 6, 37, 37, 37, 37, 37, 30, 26, 30, 30, 6, 6, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 6] 50 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610919887 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 Building ZINC001610919887 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610919887 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 590) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1) `ZINC001610919887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610919887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001610919887 none CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 26, 30, 30, 26, 6, 4, 6, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 6, 6, 6, 37, 37, 37, 37, 37, 30, 26, 30, 30, 6, 6, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 6] 50 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 591) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1) `ZINC001610919887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610919887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001610919887 none CCc1ccccc1Oc1ccc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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.3', 'C.3', 'C.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 26, 30, 30, 26, 6, 5, 6, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 6, 6, 6, 37, 37, 37, 37, 37, 30, 26, 30, 30, 6, 6, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 6] 50 rigid atoms, others: [14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610919887 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610919887 Building ZINC001610930458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610930458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/592 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C) `ZINC001610930458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610930458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610930458 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 10, 15, 15, 15, 34, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 9, 9, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/593 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C) `ZINC001610930458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610930458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610930458 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 9, 14, 14, 12, 14, 14, 14, 31, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 9, 9, 14, 14, 14, 14, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610930458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 Building ZINC001610930458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610930458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 592) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C) `ZINC001610930458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610930458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610930458 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 9, 15, 15, 10, 15, 15, 15, 34, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 9, 9, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 593) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C) `ZINC001610930458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610930458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001610930458 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Oc1cc(Cl)ccc1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 9, 14, 14, 12, 14, 14, 14, 31, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 9, 9, 14, 14, 14, 14, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610930458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610930458 Building ZINC001610941237 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610941237 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/594 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610941237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941237 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 11, 11, 21, 21, 21, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/595 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610941237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941237 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 8, 8, 8, 8, 23, 23, 23, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610941237 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 Building ZINC001610941237 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610941237 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 594) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610941237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941237 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 11, 11, 21, 21, 21, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 595) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610941237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941237 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 8, 8, 8, 8, 23, 23, 23, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610941237 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941237 Building ZINC001610941238 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610941238 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/596 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610941238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941238 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/597 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610941238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941238 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 11, 11, 11, 11, 22, 22, 22, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610941238 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 Building ZINC001610941238 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610941238 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 596) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610941238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941238 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 1, 4, 5, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 597) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(C)C) `ZINC001610941238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610941238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001610941238 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccc(F)c(F)c2)C1(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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 11, 11, 11, 11, 22, 22, 22, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 68 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610941238 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610941238 Building ZINC001610977419 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610977419 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/598 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001610977419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610977419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001610977419 none CC(C)(C)OC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 43, 36, 43, 35, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 36, 13, 13, 2, 3, 1, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/599 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001610977419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610977419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001610977419 none CC(C)(C)OC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 41, 35, 41, 34, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 13, 13, 2, 3, 1, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610977419 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 Building ZINC001610977419 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001610977419 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 598) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001610977419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001610977419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001610977419 none CC(C)(C)OC(=O)NC1(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 43, 36, 43, 35, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 35, 35, 35, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 36, 13, 13, 2, 3, 1, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 599) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1) `ZINC001610977419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001610977419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001610977419 none CC(C)(C)OC(=O)NC1(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCCCC1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 41, 35, 41, 34, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 34, 34, 34, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 13, 13, 2, 3, 1, 3, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001610977419 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001610977419 Building ZINC001611012661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611012661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/600 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001611012661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611012661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001611012661 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/601 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001611012661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611012661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001611012661 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 21, 21, 21, 21, 21, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611012661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 Building ZINC001611012661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611012661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 600) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001611012661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611012661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001611012661 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 601) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001611012661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611012661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001611012661 none O=C(NCc1ccc(Br)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 21, 21, 21, 21, 21, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611012661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611012661 Building ZINC001611117267 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611117267 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/602 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611117267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611117267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611117267 none COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 7, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 3, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/603 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611117267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611117267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611117267 none COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 7, 31, 31, 31, 31, 31, 5, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611117267 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 Building ZINC001611117267 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611117267 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 602) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611117267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611117267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611117267 none COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 7, 29, 29, 29, 29, 29, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 3, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 603) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611117267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611117267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611117267 none COC(=O)c1cc(C2CCCCC2)sc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 7, 31, 31, 31, 31, 31, 5, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 10, 10, 10, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611117267 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611117267 Building ZINC001611173068 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611173068 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/604 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1) `ZINC001611173068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611173068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611173068 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 51 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/605 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1) `ZINC001611173068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611173068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611173068 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 2, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611173068 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 Building ZINC001611173068 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611173068 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 604) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1) `ZINC001611173068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611173068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611173068 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 51 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 605) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1) `ZINC001611173068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611173068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611173068 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC2(CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 2, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611173068 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611173068 Building ZINC001611209601 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611209601 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/606 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1) `ZINC001611209601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611209601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 2, 2, 2, 17, 17, 7, 17, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/607 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1) `ZINC001611209601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611209601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 8, 8, 8, 6, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611209601 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 Building ZINC001611209601 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611209601 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 606) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1) `ZINC001611209601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611209601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 2, 2, 2, 17, 17, 7, 17, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 607) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1) `ZINC001611209601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611209601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 8, 8, 8, 6, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611209601 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209601 Building ZINC001611209602 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611209602 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/608 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1) `ZINC001611209602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611209602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/609 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1) `ZINC001611209602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611209602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611209602 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 Building ZINC001611209602 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611209602 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 608) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1) `ZINC001611209602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611209602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 609) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1) `ZINC001611209602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611209602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611209602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611209602 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611209602 Building ZINC001611236937 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611236937 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/610 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001611236937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611236937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001611236937 none CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 10, 10, 9, 10, 10, 10, 10, 25, 28, 28, 27, 28, 28, 28, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 7, 7, 10, 10, 10, 28, 28, 28, 28, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/611 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001611236937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611236937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001611236937 none CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 24, 27, 27, 24, 24, 27, 27, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 27, 27, 27, 27, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611236937 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 Building ZINC001611236937 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611236937 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 610) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001611236937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611236937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001611236937 none CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 10, 10, 9, 10, 10, 10, 10, 25, 28, 28, 27, 28, 28, 28, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 7, 7, 10, 10, 10, 28, 28, 28, 28, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 611) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001611236937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611236937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001611236937 none CCN(Cc1ccc(Cl)cc1Oc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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: [5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 9, 9, 9, 9, 9, 9, 9, 24, 27, 27, 24, 24, 27, 27, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 27, 27, 27, 27, 3, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611236937 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611236937 Building ZINC001611259346 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611259346 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/612 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/612' -> `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)c1nc(c2ccccc2C)cs1) `ZINC001611259346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611259346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001611259346 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 9, 9, 9, 9, 9, 3, 13, 13, 13, 39, 39, 13, 39, 39, 39, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 39, 39, 13, 39, 39, 39, 39, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/613 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/613' -> `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)c1nc(c2ccccc2C)cs1) `ZINC001611259346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611259346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001611259346 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 9, 9, 8, 9, 9, 3, 13, 13, 13, 38, 38, 19, 38, 38, 38, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 38, 38, 18, 38, 38, 38, 38, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 120 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611259346 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 Building ZINC001611259346 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611259346 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 612) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1) `ZINC001611259346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611259346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001611259346 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 9, 9, 9, 9, 9, 3, 13, 13, 13, 39, 39, 13, 39, 39, 39, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 39, 39, 13, 39, 39, 39, 39, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 613) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1) `ZINC001611259346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611259346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001611259346 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc(c2ccccc2C)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 9, 9, 8, 9, 9, 3, 13, 13, 13, 38, 38, 19, 38, 38, 38, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 38, 38, 18, 38, 38, 38, 38, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 120 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611259346 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611259346 Building ZINC001611268766 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611268766 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/614 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611268766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611268766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001611268766 none O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9] 35 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/615 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611268766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611268766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001611268766 none O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [7, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611268766 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 Building ZINC001611268766 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611268766 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 614) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611268766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611268766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001611268766 none O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9] 35 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 615) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001611268766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611268766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001611268766 none O=C(N1CCCc2cc(C(F)(F)F)cc(Cl)c21)[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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 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: [7, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611268766 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611268766 Building ZINC001611321696 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611321696 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/616 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001611321696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611321696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001611321696 none O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 26, 26, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 26, 26, 38, 38, 38, 38, 26, 26, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/617 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001611321696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611321696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001611321696 none O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 26, 26, 14, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 26, 26, 38, 38, 38, 38, 26, 26, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611321696 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 Building ZINC001611321696 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611321696 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 616) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001611321696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611321696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001611321696 none O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 26, 26, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 26, 26, 38, 38, 38, 38, 26, 26, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 617) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001611321696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611321696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001611321696 none O=C(NCc1ccc(c2nc3ccccc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 26, 26, 14, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 3, 14, 14, 26, 26, 38, 38, 38, 38, 26, 26, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611321696 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611321696 Building ZINC001611418498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001611418498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/618 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/619 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/620 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/620' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/621 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/621' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611418498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 Building ZINC001611418498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001611418498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 618) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 619) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 620) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 621) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611418498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 Building ZINC001611418498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001611418498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 618) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 619) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 620) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 621) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611418498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 Building ZINC001611418498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001611418498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 618) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 619) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 21, 25, 25, 33, 33, 27, 33, 33, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 28, 28, 28, 28, 28, 25, 25, 25, 25, 33, 33, 33, 33, 33, 21, 21, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 620) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 621) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001611418498.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001611418498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001611418498 none CCCN(Cc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 20, 24, 24, 33, 33, 27, 33, 33, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 27, 27, 27, 24, 24, 24, 24, 33, 33, 33, 33, 33, 20, 20, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611418498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611418498 Building ZINC001611436270 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611436270 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/622 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611436270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436270 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 5, 15, 20, 20, 15, 20, 20, 5, 11, 22, 22, 22, 33, 33, 22, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 15, 15, 20, 20, 15, 20, 20, 11, 11, 66, 33, 33, 22, 33, 3, 3] 150 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]) total number of confs: 297 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/623 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611436270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436270 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 17, 21, 21, 20, 21, 21, 6, 14, 26, 26, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 17, 17, 21, 21, 21, 21, 21, 14, 14, 78, 34, 34, 26, 34, 3, 3] 150 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]) total number of confs: 302 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611436270 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 Building ZINC001611436270 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611436270 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 622) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611436270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436270 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 5, 15, 20, 20, 15, 20, 20, 5, 11, 22, 22, 22, 33, 33, 22, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 15, 15, 20, 20, 15, 20, 20, 11, 11, 66, 33, 33, 22, 33, 3, 3] 150 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]) total number of confs: 297 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 623) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611436270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436270 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 17, 21, 21, 20, 21, 21, 6, 14, 26, 26, 26, 34, 34, 26, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 17, 17, 21, 21, 21, 21, 21, 14, 14, 78, 34, 34, 26, 34, 3, 3] 150 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]) total number of confs: 302 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611436270 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436270 Building ZINC001611436271 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611436271 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/624 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611436271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436271 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 20, 20, 18, 20, 20, 6, 13, 24, 24, 24, 33, 33, 29, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 16, 16, 20, 20, 20, 20, 20, 13, 13, 72, 33, 33, 30, 33, 3, 3] 150 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]) total number of confs: 265 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/625 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611436271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436271 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 5, 15, 20, 20, 18, 20, 20, 5, 12, 22, 22, 22, 33, 33, 26, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 15, 15, 20, 20, 20, 20, 20, 12, 12, 66, 33, 33, 28, 33, 3, 3] 150 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]) total number of confs: 271 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611436271 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 Building ZINC001611436271 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611436271 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 624) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611436271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436271 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 20, 20, 18, 20, 20, 6, 13, 24, 24, 24, 33, 33, 29, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 16, 16, 20, 20, 20, 20, 20, 13, 13, 72, 33, 33, 30, 33, 3, 3] 150 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]) total number of confs: 265 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 625) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1) `ZINC001611436271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611436271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001611436271 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)C[C@H](O)c2ccccc2C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 2, 2, 5, 15, 20, 20, 18, 20, 20, 5, 12, 22, 22, 22, 33, 33, 26, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 15, 15, 20, 20, 20, 20, 20, 12, 12, 66, 33, 33, 28, 33, 3, 3] 150 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]) total number of confs: 271 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611436271 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611436271 Building ZINC001611482659 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611482659 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/626 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001611482659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611482659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001611482659 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 17, 17, 17, 17, 17, 17, 41, 41, 50, 50, 50, 17, 17, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/627 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001611482659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611482659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001611482659 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 41, 41, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611482659 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 Building ZINC001611482659 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611482659 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 626) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001611482659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611482659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001611482659 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 17, 17, 17, 17, 17, 17, 41, 41, 50, 50, 50, 17, 17, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 627) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001611482659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611482659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001611482659 none O=C(NCc1ccccc1c1ccc(Cn2cccn2)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 41, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 18, 18, 18, 18, 18, 18, 41, 41, 50, 50, 50, 18, 18, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611482659 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611482659 Building ZINC001611553577 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611553577 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/628 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611553577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553577 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 18, 18, 18, 18, 18, 18, 46, 46, 20, 27, 46, 46, 46, 46, 46, 18, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 18, 18, 18, 18, 46, 46, 46, 46, 18, 18, 4, 2, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/629 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611553577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553577 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 10, 18, 18, 18, 18, 18, 18, 44, 44, 18, 26, 44, 44, 44, 44, 44, 18, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 18, 18, 18, 18, 44, 44, 44, 44, 18, 18, 6, 1, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611553577 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 Building ZINC001611553577 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611553577 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 628) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611553577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553577 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 18, 18, 18, 18, 18, 18, 46, 46, 20, 27, 46, 46, 46, 46, 46, 18, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 18, 18, 18, 18, 46, 46, 46, 46, 18, 18, 4, 2, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 629) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611553577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553577 none O=C(N1CCO[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 10, 18, 18, 18, 18, 18, 18, 44, 44, 18, 26, 44, 44, 44, 44, 44, 18, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 18, 18, 18, 18, 44, 44, 44, 44, 18, 18, 6, 1, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611553577 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553577 Building ZINC001611553578 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611553578 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/630 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611553578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553578 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 16, 45, 45, 16, 17, 45, 45, 45, 45, 45, 16, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 16, 16, 16, 16, 45, 45, 45, 45, 16, 16, 5, 1, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/631 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611553578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553578 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 19, 19, 19, 19, 19, 19, 46, 46, 19, 19, 46, 46, 46, 46, 46, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 19, 46, 46, 46, 46, 19, 19, 4, 1, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611553578 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 Building ZINC001611553578 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611553578 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 630) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611553578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553578 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 16, 16, 16, 16, 16, 16, 45, 45, 16, 17, 45, 45, 45, 45, 45, 16, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 16, 16, 16, 16, 45, 45, 45, 45, 16, 16, 5, 1, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 631) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001611553578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611553578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001611553578 none O=C(N1CCO[C@@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 19, 19, 19, 19, 19, 19, 46, 46, 19, 19, 46, 46, 46, 46, 46, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 19, 19, 19, 46, 46, 46, 46, 19, 19, 4, 1, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611553578 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611553578 Building ZINC001611554739 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611554739 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/632 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(C)C) `ZINC001611554739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611554739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554739 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 2, 2, 2, 14, 14, 14, 14, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/633 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(C)C) `ZINC001611554739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611554739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554739 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 8, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 3, 3, 3, 28, 28, 8, 28, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611554739 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 Building ZINC001611554739 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611554739 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 632) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(C)C) `ZINC001611554739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611554739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554739 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 2, 2, 2, 14, 14, 14, 14, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 59 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 633) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(C)C) `ZINC001611554739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611554739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554739 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 8, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 3, 3, 3, 28, 28, 8, 28, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611554739 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554739 Building ZINC001611554743 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611554743 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/634 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(C)C) `ZINC001611554743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611554743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554743 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 82 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/635 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(C)C) `ZINC001611554743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611554743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554743 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 82 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611554743 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 Building ZINC001611554743 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611554743 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 634) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(C)C) `ZINC001611554743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611554743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554743 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 82 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 635) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(C)C) `ZINC001611554743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611554743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611554743 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CC=CC2)[C@H]1C(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 82 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611554743 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611554743 Building ZINC001611568650 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611568650 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/636 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F) `ZINC001611568650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611568650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001611568650 none Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [24, 24, 24, 16, 24, 24, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 31, 31, 24, 24, 24, 24, 16, 24, 24, 8, 4, 9, 9, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/637 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F) `ZINC001611568650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611568650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001611568650 none Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [25, 25, 25, 16, 25, 25, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 31, 31, 25, 25, 25, 25, 16, 25, 25, 8, 4, 8, 8, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611568650 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 Building ZINC001611568650 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611568650 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 636) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F) `ZINC001611568650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611568650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001611568650 none Cc1ccccc1n1ncc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [24, 24, 24, 16, 24, 24, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 31, 31, 24, 24, 24, 24, 16, 24, 24, 8, 4, 9, 9, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 637) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F) `ZINC001611568650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611568650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001611568650 none Cc1ccccc1n1ncc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [25, 25, 25, 16, 25, 25, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 31, 31, 25, 25, 25, 25, 16, 25, 25, 8, 4, 8, 8, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611568650 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611568650 Building ZINC001611606194 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611606194 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/638 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C) `ZINC001611606194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611606194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611606194 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 37, 37, 5, 37, 37, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 37, 37, 7, 37, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/639 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C) `ZINC001611606194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611606194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611606194 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 4, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 34, 34, 15, 34, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611606194 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 Building ZINC001611606194 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001611606194 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 638) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C) `ZINC001611606194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611606194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611606194 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 37, 37, 5, 37, 37, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 37, 37, 7, 37, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 639) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C) `ZINC001611606194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611606194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611606194 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 34, 34, 4, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 34, 34, 15, 34, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001611606194 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001611606194 Building ZINC000009727080 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009727080 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/640 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1) `ZINC000009727080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009727080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000009727080 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 32, 32, 32, 32, 32, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/641 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1) `ZINC000009727080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009727080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000009727080 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 31, 31, 31, 31, 31, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC000009727080 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 Building ZINC000009727080 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009727080 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 640) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1) `ZINC000009727080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009727080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000009727080 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 32, 32, 32, 32, 32, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 641) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1) `ZINC000009727080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009727080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000009727080 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(c2c[nH]c3ccccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 31, 31, 31, 31, 31, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC000009727080 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC000009727080 Building ZINC001614945366 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614945366 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/642 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1) `ZINC001614945366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614945366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001614945366 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 39, 32, 29, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 39, 29, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50] 50 rigid atoms, others: [50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/643 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1) `ZINC001614945366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614945366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001614945366 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 38, 31, 29, 31, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 38, 29, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50] 50 rigid atoms, others: [50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001614945366 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 Building ZINC001614945366 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614945366 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 642) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1) `ZINC001614945366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614945366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001614945366 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 39, 32, 29, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 39, 29, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50] 50 rigid atoms, others: [50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 643) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1) `ZINC001614945366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614945366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001614945366 none Cc1ccc(NC(=O)Nc2cccc3c2CCN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 38, 31, 29, 31, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 38, 29, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50] 50 rigid atoms, others: [50, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 53, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001614945366 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001614945366 Building ZINC001616192940 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616192940 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/644 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/645 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/646 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/646' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/647 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/647' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616192940 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 Building ZINC001616192940 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616192940 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 644) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 645) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 646) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 647) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616192940 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 Building ZINC001616192940 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616192940 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 644) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 645) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 646) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 647) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616192940 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 Building ZINC001616192940 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616192940 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 644) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 645) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 35, 35, 33, 35, 35, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 646) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 647) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1) `ZINC001616192940.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616192940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001616192940 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CN(Cc2ccccc2)C[C@H]1c1ccccc1 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', 'C.2', 'Cl', 'S.3', 'C.3', 'N.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 4, 6, 6, 12, 12, 30, 30, 36, 36, 36, 36, 36, 12, 12, 13, 13, 13, 13, 13] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616192940 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616192940 Building ZINC001616193226 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616193226 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/648 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616193226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616193226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001616193226 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/649 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616193226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616193226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001616193226 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 38, 38, 38, 38, 38, 38, 24, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616193226 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 Building ZINC001616193226 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616193226 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 648) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616193226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616193226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001616193226 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 649) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616193226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616193226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001616193226 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 38, 38, 38, 38, 38, 38, 24, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 38, 38, 38, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616193226 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616193226 Building ZINC001616309037 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616309037 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/650 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616309037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616309037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001616309037 none O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 7, 26, 31, 31, 31, 31, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 31, 31, 7, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/651 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616309037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616309037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001616309037 none O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 7, 26, 31, 31, 31, 31, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 31, 31, 7, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616309037 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 Building ZINC001616309037 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616309037 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 650) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616309037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616309037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001616309037 none O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 7, 26, 31, 31, 31, 31, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 31, 31, 7, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 651) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616309037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616309037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001616309037 none O=C(Nc1nc2ccc(OCC(F)(F)F)cc2s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 7, 7, 26, 31, 31, 31, 31, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 31, 31, 7, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616309037 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616309037 Building ZINC001616311840 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616311840 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/652 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616311840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616311840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001616311840 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 5, 34, 35, 35, 35, 5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 2, 5, 5, 5, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/653 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616311840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616311840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001616311840 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 35, 35, 35, 35, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616311840 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 Building ZINC001616311840 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616311840 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 652) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616311840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616311840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001616311840 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 5, 34, 35, 35, 35, 5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 2, 5, 5, 5, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 653) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616311840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616311840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001616311840 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 35, 35, 35, 35, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616311840 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616311840 Building ZINC001616317541 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616317541 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/654 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616317541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616317541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616317541 none O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 9, 9, 4, 4, 22, 28, 28, 9, 9, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 28, 9, 9, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/655 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616317541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616317541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616317541 none O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 9, 9, 4, 4, 20, 28, 28, 9, 9, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 28, 9, 9, 4, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616317541 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 Building ZINC001616317541 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616317541 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 654) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616317541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616317541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616317541 none O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 9, 9, 4, 4, 22, 28, 28, 9, 9, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 28, 9, 9, 4, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 655) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616317541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616317541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616317541 none O=C(Nc1nc(c2ccc(OC(F)F)cc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 9, 9, 4, 4, 20, 28, 28, 9, 9, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 28, 9, 9, 4, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616317541 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616317541 Building ZINC001616330902 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616330902 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/656 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616330902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330902 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 13, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/657 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616330902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330902 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 23, 25, 25, 23, 23, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 2, 9, 9, 13, 13, 13, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616330902 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 Building ZINC001616330902 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616330902 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 656) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616330902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330902 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 13, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 657) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616330902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330902 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 23, 25, 25, 23, 23, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 2, 9, 9, 13, 13, 13, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616330902 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330902 Building ZINC001616330908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616330908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/658 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616330908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330908 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 23, 25, 25, 23, 23, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 13, 13, 13, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/659 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616330908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330908 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 28, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 13, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616330908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 Building ZINC001616330908 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616330908 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 658) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616330908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330908 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 23, 25, 25, 23, 23, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 13, 13, 13, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 659) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)cc2)cc1Cl) `ZINC001616330908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616330908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001616330908 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Sc2ccc(Br)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.3', 'H', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 28, 29, 29, 29, 29, 29, 29, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 13, 13, 13, 29, 29, 29, 29, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616330908 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616330908 Building ZINC001616421169 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616421169 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/660 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/660' -> `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@]1(C)Cc1cccc(Cl)c1) `ZINC001616421169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616421169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 18, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 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]) total number of confs: 106 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/661 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/661' -> `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@]1(C)Cc1cccc(Cl)c1) `ZINC001616421169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616421169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616421169 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 Building ZINC001616421169 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616421169 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 660) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)c1) `ZINC001616421169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616421169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 18, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 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]) total number of confs: 106 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 661) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)c1) `ZINC001616421169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616421169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616421169 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421169 Building ZINC001616421170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616421170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/662 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/662' -> `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@@]1(C)Cc1cccc(Cl)c1) `ZINC001616421170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616421170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421170 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/663 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/663' -> `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@@]1(C)Cc1cccc(Cl)c1) `ZINC001616421170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616421170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421170 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616421170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 Building ZINC001616421170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616421170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 662) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)c1) `ZINC001616421170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616421170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421170 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 8, 8, 21, 39, 39, 39, 39, 39, 39, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 663) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)c1) `ZINC001616421170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616421170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001616421170 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1cccc(Cl)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', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616421170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616421170 Building ZINC001616476837 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616476837 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/664 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616476837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476837 none CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 17, 49, 10, 17, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 28, 28, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 2, 1, 2, 28, 28, 17, 28, 28] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/665 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616476837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476837 none CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 17, 45, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 25, 25, 17, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 17, 17, 17, 9, 9, 2, 3, 1, 3, 25, 25, 17, 25, 25] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616476837 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 Building ZINC001616476837 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616476837 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 664) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616476837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476837 none CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 17, 49, 10, 17, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 28, 28, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 2, 2, 1, 2, 28, 28, 17, 28, 28] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 665) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616476837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476837 none CC(C)(C)OC(=O)[C@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 17, 45, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 25, 25, 17, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 17, 17, 17, 9, 9, 2, 3, 1, 3, 25, 25, 17, 25, 25] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616476837 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476837 Building ZINC001616476840 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616476840 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/666 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616476840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476840 none CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 17, 48, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 24, 24, 17, 24, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 17, 9, 9, 2, 3, 1, 3, 24, 24, 23, 24, 24] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/667 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616476840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476840 none CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 18, 50, 11, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 29, 29, 18, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 11, 11, 2, 2, 1, 2, 29, 29, 18, 29, 29] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616476840 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 Building ZINC001616476840 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616476840 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 666) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616476840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476840 none CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 17, 48, 9, 15, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 24, 24, 17, 24, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 17, 17, 9, 9, 2, 3, 1, 3, 24, 24, 23, 24, 24] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 667) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001616476840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616476840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616476840 none CC(C)(C)OC(=O)[C@@](C)(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 18, 50, 11, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 29, 29, 18, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 11, 11, 2, 2, 1, 2, 29, 29, 18, 29, 29] 50 rigid atoms, others: [11, 14, 13, 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616476840 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616476840 Building ZINC001616488303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616488303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/668 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 29, 29, 29, 29, 29, 46, 50, 50, 46, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 29, 2, 1, 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/669 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 30, 30, 30, 30, 30, 47, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/670 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/670' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 46, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/671 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/671' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 2, 1, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616488303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 Building ZINC001616488303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616488303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 668) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 29, 29, 29, 29, 29, 46, 50, 50, 46, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 29, 2, 1, 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 669) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 30, 30, 30, 30, 30, 47, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 670) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 46, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 671) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 2, 1, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616488303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 Building ZINC001616488303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616488303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 668) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 29, 29, 29, 29, 29, 46, 50, 50, 46, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 29, 2, 1, 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 669) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 30, 30, 30, 30, 30, 47, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 670) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 46, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 671) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 2, 1, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616488303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 Building ZINC001616488303 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001616488303 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 668) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 29, 29, 29, 29, 29, 46, 50, 50, 46, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 29, 2, 1, 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 669) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 30, 30, 30, 30, 30, 47, 50, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 670) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 46, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 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]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 671) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001616488303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001616488303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001616488303 none O=C(NC[C@H]1CC[N@@](Cc2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 28, 28, 28, 28, 28, 46, 50, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 10, 10, 28, 28, 28, 28, 46, 46, 50, 50, 50, 50, 28, 28, 28, 28, 2, 1, 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616488303 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616488303 Building ZINC001616492349 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616492349 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/672 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616492349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492349 none O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 41, 41, 20, 41, 41, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 20, 41, 41, 34, 41, 41, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/673 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616492349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492349 none O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 36, 36, 22, 36, 36, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 22, 36, 36, 30, 36, 36, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616492349 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 Building ZINC001616492349 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616492349 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 672) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616492349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492349 none O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 41, 41, 20, 41, 41, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 20, 41, 41, 34, 41, 41, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 673) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616492349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492349 none O=C(N1CCCC[C@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 36, 36, 22, 36, 36, 22, 22, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 22, 36, 36, 30, 36, 36, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616492349 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492349 Building ZINC001616492351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616492351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/674 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616492351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492351 none O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 37, 37, 33, 37, 37, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 20, 37, 37, 34, 37, 37, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/675 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616492351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492351 none O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 42, 42, 38, 42, 42, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 22, 42, 42, 40, 42, 42, 7, 7] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616492351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 Building ZINC001616492351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616492351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 674) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616492351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492351 none O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 37, 37, 33, 37, 37, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 20, 37, 37, 34, 37, 37, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 675) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001616492351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616492351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001616492351 none O=C(N1CCCC[C@@H]1c1ncc(c2ccccc2)[nH]1)[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', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', '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, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 42, 42, 38, 42, 42, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 22, 42, 42, 40, 42, 42, 7, 7] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616492351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616492351 Building ZINC001616627021 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616627021 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/676 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1) `ZINC001616627021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616627021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001616627021 none CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 14, 14, 23, 23, 14, 8, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 16, 16, 16, 16, 25, 16, 16, 16, 23, 23, 31, 31, 31, 31, 31, 23, 23, 14, 14, 2, 2, 4, 2, 2, 16, 16, 25, 25, 25, 16, 23, 23] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/677 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1) `ZINC001616627021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616627021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001616627021 none CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 25, 19, 25, 25, 15, 8, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 16, 16, 16, 16, 24, 16, 16, 16, 25, 25, 35, 35, 35, 35, 35, 25, 25, 15, 15, 2, 2, 4, 2, 2, 16, 16, 24, 24, 24, 16, 25, 25] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616627021 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 Building ZINC001616627021 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616627021 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 676) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1) `ZINC001616627021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616627021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001616627021 none CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 14, 14, 23, 23, 14, 8, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 16, 16, 16, 16, 25, 16, 16, 16, 23, 23, 31, 31, 31, 31, 31, 23, 23, 14, 14, 2, 2, 4, 2, 2, 16, 16, 25, 25, 25, 16, 23, 23] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 677) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1) `ZINC001616627021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616627021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001616627021 none CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 25, 19, 25, 25, 15, 8, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 16, 16, 16, 16, 24, 16, 16, 16, 25, 25, 35, 35, 35, 35, 35, 25, 25, 15, 15, 2, 2, 4, 2, 2, 16, 16, 24, 24, 24, 16, 25, 25] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616627021 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616627021 Building ZINC001616788079 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616788079 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/678 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001616788079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616788079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001616788079 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 4, 8, 14, 14, 14, 8, 14, 14, 14, 23, 26, 26, 26, 26, 26, 26, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 14, 14, 14, 26, 26, 26, 26, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/679 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001616788079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616788079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001616788079 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 4, 8, 14, 14, 14, 12, 14, 14, 14, 23, 26, 26, 26, 26, 26, 26, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 14, 14, 14, 26, 26, 26, 26, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616788079 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 Building ZINC001616788079 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616788079 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 678) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001616788079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616788079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001616788079 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 4, 8, 14, 14, 14, 8, 14, 14, 14, 23, 26, 26, 26, 26, 26, 26, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 14, 14, 14, 26, 26, 26, 26, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 679) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)cc2)cn1) `ZINC001616788079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616788079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001616788079 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2cc(Cl)ccc2Oc2ccc(Cl)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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 4, 8, 14, 14, 14, 12, 14, 14, 14, 23, 26, 26, 26, 26, 26, 26, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 4, 8, 8, 14, 14, 14, 26, 26, 26, 26, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616788079 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616788079 Building ZINC001616812979 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616812979 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/680 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616812979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812979 none O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/681 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616812979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812979 none O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616812979 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 Building ZINC001616812979 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616812979 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 680) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616812979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812979 none O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 681) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616812979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812979 none O=C(N1CCO[C@@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616812979 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812979 Building ZINC001616812980 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616812980 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/682 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616812980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812980 none O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/683 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616812980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812980 none O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 5, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 25, 25, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616812980 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 Building ZINC001616812980 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616812980 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 682) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616812980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812980 none O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 11, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 683) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616812980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616812980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001616812980 none O=C(N1CCO[C@H](c2cc(F)c(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 15, 1, 16, 1, 1, 16, 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] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 5, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 25, 25, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616812980 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616812980 Building ZINC001616846130 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616846130 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/684 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/684' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001616846130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616846130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846130 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [10, 8, 4, 8, 8, 16, 26, 26, 16, 26, 26, 26, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 16, 16, 26, 26, 25, 26, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/685 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/685' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001616846130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616846130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846130 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [9, 6, 2, 6, 6, 17, 28, 28, 17, 28, 28, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 17, 17, 28, 28, 25, 28, 2, 2, 2, 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]) total number of confs: 157 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616846130 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 Building ZINC001616846130 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616846130 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 684) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616846130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616846130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846130 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [10, 8, 4, 8, 8, 16, 26, 26, 16, 26, 26, 26, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 16, 16, 26, 26, 25, 26, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 685) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616846130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616846130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846130 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [9, 6, 2, 6, 6, 17, 28, 28, 17, 28, 28, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 17, 17, 28, 28, 25, 28, 2, 2, 2, 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]) total number of confs: 157 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616846130 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846130 Building ZINC001616846131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616846131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/686 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/686' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001616846131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616846131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846131 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [9, 6, 2, 6, 6, 17, 28, 28, 17, 28, 28, 28, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 17, 17, 28, 28, 24, 28, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/687 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/687' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001616846131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616846131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846131 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [10, 8, 4, 8, 8, 16, 26, 26, 25, 26, 26, 26, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 16, 16, 26, 26, 25, 26, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616846131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 Building ZINC001616846131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616846131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 686) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616846131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616846131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846131 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [9, 6, 2, 6, 6, 17, 28, 28, 17, 28, 28, 28, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 17, 17, 28, 28, 24, 28, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 687) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001616846131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616846131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001616846131 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [10, 8, 4, 8, 8, 16, 26, 26, 25, 26, 26, 26, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 16, 16, 26, 26, 25, 26, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616846131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616846131 Building ZINC001616932038 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616932038 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/688 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/688' -> `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)NCC(C)(C)c1ccccc1) `ZINC001616932038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616932038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616932038 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/689 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/689' -> `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)NCC(C)(C)c1ccccc1) `ZINC001616932038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616932038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616932038 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 12, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616932038 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 Building ZINC001616932038 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616932038 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 688) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1) `ZINC001616932038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616932038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616932038 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 689) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1) `ZINC001616932038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616932038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616932038 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 12, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616932038 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616932038 Building ZINC001616966958 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616966958 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/690 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001616966958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616966958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966958 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 2, 6, 6, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/691 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001616966958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616966958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966958 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 12, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 10, 10, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616966958 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 Building ZINC001616966958 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616966958 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 690) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001616966958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616966958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966958 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 2, 6, 6, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 691) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1) `ZINC001616966958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616966958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966958 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 12, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 10, 10, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616966958 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966958 Building ZINC001616966960 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616966960 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/692 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/692' -> `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)NCC[C@H]1CCC(F)(F)C1) `ZINC001616966960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616966960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966960 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 9, 9, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/693 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/693' -> `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)NCC[C@H]1CCC(F)(F)C1) `ZINC001616966960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616966960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966960 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 14, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 13, 13, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616966960 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 Building ZINC001616966960 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616966960 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 692) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001616966960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616966960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966960 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 7, 7, 9, 9, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 693) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1) `ZINC001616966960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616966960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616966960 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 14, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 13, 13, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001616966960 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001616966960 Building ZINC001617011329 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617011329 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/694 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001617011329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617011329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001617011329 none O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 23, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 23, 23, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/695 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001617011329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617011329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001617011329 none O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 23, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 23, 23, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617011329 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 Building ZINC001617011329 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617011329 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 694) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001617011329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617011329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001617011329 none O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 23, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 23, 23, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 695) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001617011329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617011329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001617011329 none O=C(Nc1ccc(=O)n(Cc2cccc(Cl)c2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 11, 11, 11, 11, 23, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 23, 23, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/11891/xbl-8058088.38/working/building/ZINC001617011329 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617011329 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617011329 Building ZINC001617012253 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617012253 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/696 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F) `ZINC001617012253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617012253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001617012253 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F 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.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 33, 44, 44, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 3, 7, 33, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/697 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F) `ZINC001617012253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617012253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001617012253 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F 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.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 33, 44, 44, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 3, 7, 33, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617012253 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 Building ZINC001617012253 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617012253 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 696) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F) `ZINC001617012253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617012253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001617012253 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F 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.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 33, 44, 44, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 3, 7, 33, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 697) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F) `ZINC001617012253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617012253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001617012253 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)c(F)c(F)c1F 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.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 33, 44, 44, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 3, 7, 33, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617012253 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617012253 Building ZINC001617108647 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617108647 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/698 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617108647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617108647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001617108647 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 15, 17, 17, 15, 15, 30, 30, 30, 30, 30, 30, 30, 17, 17, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 17, 17, 30, 30, 30, 30, 30, 30, 30, 17, 17, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/699 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617108647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617108647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001617108647 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 15, 18, 18, 15, 16, 31, 31, 31, 31, 31, 31, 31, 18, 18, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 18, 18, 31, 31, 31, 31, 31, 31, 31, 18, 18, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617108647 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 Building ZINC001617108647 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617108647 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 698) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617108647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617108647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001617108647 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 15, 17, 17, 15, 15, 30, 30, 30, 30, 30, 30, 30, 17, 17, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 17, 17, 30, 30, 30, 30, 30, 30, 30, 17, 17, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 699) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617108647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617108647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001617108647 none CN(CCOc1ccc(OCc2ccccc2)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 15, 18, 18, 15, 16, 31, 31, 31, 31, 31, 31, 31, 18, 18, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 18, 18, 31, 31, 31, 31, 31, 31, 31, 18, 18, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617108647 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617108647 Building ZINC001617138230 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617138230 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/700 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001617138230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617138230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001617138230 none COc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 18, 18, 33, 33, 33, 18, 18, 10, 6, 6, 6, 6] 43 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/701 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001617138230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617138230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001617138230 none COc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [34, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 34, 34, 34, 19, 19, 11, 6, 6, 6, 6] 44 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617138230 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 Building ZINC001617138230 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617138230 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 700) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001617138230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617138230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001617138230 none COc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 6, 6, 6, 18, 18, 33, 33, 33, 18, 18, 10, 6, 6, 6, 6] 43 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 701) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21) `ZINC001617138230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617138230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001617138230 none COc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [34, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 19, 19, 34, 34, 34, 19, 19, 11, 6, 6, 6, 6] 44 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617138230 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617138230 Building ZINC001617229087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617229087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/702 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001617229087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617229087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617229087 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 11, 10, 7, 5, 7, 11, 12, 12, 11, 12, 12, 12, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 11, 11, 10, 10, 11, 11, 12, 12, 12, 12, 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: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/703 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001617229087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617229087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617229087 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 24, 10, 9, 6, 4, 6, 10, 11, 11, 10, 10, 11, 11, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 10, 10, 9, 9, 10, 10, 11, 11, 11, 11, 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: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617229087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 Building ZINC001617229087 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617229087 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 702) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001617229087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617229087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617229087 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 24, 24, 11, 10, 7, 5, 7, 11, 12, 12, 11, 12, 12, 12, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 11, 11, 10, 10, 11, 11, 12, 12, 12, 12, 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: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 703) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001617229087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617229087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617229087 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 23, 24, 10, 9, 6, 4, 6, 10, 11, 11, 10, 10, 11, 11, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 10, 10, 9, 9, 10, 10, 11, 11, 11, 11, 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: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617229087 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617229087 Building ZINC001617256529 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617256529 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/704 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 27, 31, 31, 29, 31, 31, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 6, 14, 14, 14, 14, 27, 27, 31, 31, 31, 31, 31, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/705 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 26, 30, 30, 26, 30, 30, 13, 13, 9, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 26, 26, 30, 30, 26, 30, 30, 13, 13, 13, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/706 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/706' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 30, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 30, 30, 33, 33, 33, 33, 33, 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]) total number of confs: 160 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/707 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/707' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 29, 32, 32, 29, 32, 32, 15, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 15, 15, 15, 15, 29, 29, 32, 32, 29, 32, 32, 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]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617256529 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 Building ZINC001617256529 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617256529 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 704) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 27, 31, 31, 29, 31, 31, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 6, 14, 14, 14, 14, 27, 27, 31, 31, 31, 31, 31, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 705) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 26, 30, 30, 26, 30, 30, 13, 13, 9, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 26, 26, 30, 30, 26, 30, 30, 13, 13, 13, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 706) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 30, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 30, 30, 33, 33, 33, 33, 33, 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]) total number of confs: 160 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 707) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 29, 32, 32, 29, 32, 32, 15, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 15, 15, 15, 15, 29, 29, 32, 32, 29, 32, 32, 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]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617256529 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 Building ZINC001617256529 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617256529 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 704) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 27, 31, 31, 29, 31, 31, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 6, 14, 14, 14, 14, 27, 27, 31, 31, 31, 31, 31, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 705) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 26, 30, 30, 26, 30, 30, 13, 13, 9, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 26, 26, 30, 30, 26, 30, 30, 13, 13, 13, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 706) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 30, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 30, 30, 33, 33, 33, 33, 33, 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]) total number of confs: 160 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 707) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 29, 32, 32, 29, 32, 32, 15, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 15, 15, 15, 15, 29, 29, 32, 32, 29, 32, 32, 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]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617256529 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 Building ZINC001617256529 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617256529 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 704) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 27, 31, 31, 29, 31, 31, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 6, 14, 14, 14, 14, 27, 27, 31, 31, 31, 31, 31, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 705) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 26, 30, 30, 26, 30, 30, 13, 13, 9, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 26, 26, 30, 30, 26, 30, 30, 13, 13, 13, 13] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 706) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 30, 33, 33, 33, 33, 33, 15, 15, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 30, 30, 33, 33, 33, 33, 33, 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]) total number of confs: 160 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 707) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001617256529.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617256529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001617256529 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 29, 32, 32, 29, 32, 32, 15, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 15, 15, 15, 15, 29, 29, 32, 32, 29, 32, 32, 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]) total number of confs: 163 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617256529 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617256529 Building ZINC001617446763 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617446763 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/708 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617446763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446763 none O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 3, 9, 9, 18, 21, 21, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 9, 8, 18, 18, 33, 33, 33, 33, 33, 33, 33, 9, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/709 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617446763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446763 none O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 17, 21, 21, 32, 34, 34, 32, 34, 34, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 10, 10, 10, 17, 17, 32, 32, 34, 34, 32, 34, 34, 10, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617446763 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 Building ZINC001617446763 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617446763 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 708) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617446763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446763 none O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 3, 9, 9, 18, 21, 21, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 9, 8, 18, 18, 33, 33, 33, 33, 33, 33, 33, 9, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 709) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617446763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446763 none O=C(Nc1cccc(C[S@@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 17, 21, 21, 32, 34, 34, 32, 34, 34, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 10, 10, 10, 17, 17, 32, 32, 34, 34, 32, 34, 34, 10, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617446763 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446763 Building ZINC001617446764 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617446764 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/710 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617446764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446764 none O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 3, 11, 11, 18, 22, 22, 33, 35, 35, 33, 35, 35, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 3, 18, 18, 33, 33, 35, 35, 33, 35, 35, 11, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/711 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617446764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446764 none O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 18, 22, 22, 34, 34, 34, 34, 34, 34, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 10, 10, 10, 18, 18, 34, 34, 34, 34, 34, 34, 34, 10, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617446764 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 Building ZINC001617446764 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617446764 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 710) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617446764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446764 none O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 3, 11, 11, 18, 22, 22, 33, 35, 35, 33, 35, 35, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 3, 18, 18, 33, 33, 35, 35, 33, 35, 35, 11, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 711) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617446764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617446764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617446764 none O=C(Nc1cccc(C[S@](=O)Cc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 10, 18, 22, 22, 34, 34, 34, 34, 34, 34, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 10, 10, 10, 18, 18, 34, 34, 34, 34, 34, 34, 34, 10, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617446764 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617446764 Building ZINC001617731154 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617731154 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/712 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617731154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617731154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001617731154 none O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 40, 40, 40, 40, 40, 42, 42, 41, 42, 42, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 2, 15, 15, 40, 40, 42, 42, 42, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/713 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617731154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617731154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001617731154 none O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 40, 40, 41, 41, 41, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617731154 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 Building ZINC001617731154 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617731154 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 712) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617731154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617731154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001617731154 none O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 40, 40, 40, 40, 40, 42, 42, 41, 42, 42, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 2, 15, 15, 40, 40, 42, 42, 42, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 713) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617731154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617731154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001617731154 none O=C(NC[C@@H]1C[C@H]1c1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 40, 40, 41, 41, 41, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617731154 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617731154 Building ZINC001617854441 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617854441 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/714 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F) `ZINC001617854441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617854441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617854441 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 32, 34, 34, 34, 34, 13, 27, 29, 29, 29, 29, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 13, 34, 34, 34, 34, 29, 29, 29, 29] 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: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/715 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F) `ZINC001617854441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617854441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617854441 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 6, 6, 6, 13, 25, 28, 28, 28, 28, 13, 31, 33, 33, 33, 33, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 6, 13, 28, 28, 28, 28, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617854441 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 Building ZINC001617854441 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617854441 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 714) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F) `ZINC001617854441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617854441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617854441 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 32, 34, 34, 34, 34, 13, 27, 29, 29, 29, 29, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 6, 13, 34, 34, 34, 34, 29, 29, 29, 29] 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: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 715) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F) `ZINC001617854441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617854441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617854441 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(CCC(F)(F)F)CCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 6, 6, 6, 13, 25, 28, 28, 28, 28, 13, 31, 33, 33, 33, 33, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 6, 13, 28, 28, 28, 28, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001617854441 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001617854441 Building ZINC001618124795 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618124795 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/716 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1) `ZINC001618124795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618124795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618124795 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 24, 39, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 24, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/717 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1) `ZINC001618124795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618124795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618124795 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 22, 37, 50, 50, 50, 50, 50, 50, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618124795 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 Building ZINC001618124795 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618124795 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 716) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1) `ZINC001618124795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618124795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618124795 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 24, 39, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 24, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 717) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1) `ZINC001618124795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618124795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618124795 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(CNC(=O)OC(C)(C)C)cc(C(F)(F)F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 22, 37, 50, 50, 50, 50, 50, 50, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618124795 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618124795 Building ZINC001618131131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001618131131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/718 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/719 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 7, 11, 4, 9, 9, 33, 33, 33, 33] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/720 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/720' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/721 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/721' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 4, 9, 9, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618131131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 Building ZINC001618131131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001618131131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 718) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 719) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 7, 11, 4, 9, 9, 33, 33, 33, 33] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 720) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 721) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 4, 9, 9, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618131131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 Building ZINC001618131131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001618131131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 718) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 719) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 7, 11, 4, 9, 9, 33, 33, 33, 33] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 720) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 721) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 4, 9, 9, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618131131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 Building ZINC001618131131 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001618131131 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 718) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 719) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 7, 11, 4, 9, 9, 33, 33, 33, 33] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 720) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 4, 9, 9, 32, 32, 32, 32] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 721) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001618131131.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001618131131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618131131 none C[C@H]1CC[N@@](c2ccc(F)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 4, 9, 9, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618131131 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618131131 Building ZINC001618348705 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348705 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/722 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348705 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 5, 13, 13, 13, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 6, 10, 10, 6, 10, 10, 6, 13, 13, 13, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/723 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348705 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 6, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 6, 12, 12, 6, 12, 12, 6, 12, 12, 12, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 119 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618348705 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 Building ZINC001618348705 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348705 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 722) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348705 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 5, 13, 13, 13, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 6, 10, 10, 6, 10, 10, 6, 13, 13, 13, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 723) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348705 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 6, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 6, 12, 12, 6, 12, 12, 6, 12, 12, 12, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 119 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618348705 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348705 Building ZINC001618348706 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348706 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/724 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348706 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 5, 10, 10, 5, 6, 12, 12, 12, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 10, 5, 12, 12, 12, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/725 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348706 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 5, 13, 13, 13, 19, 21, 21, 19, 19, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 6, 9, 9, 7, 9, 9, 6, 13, 13, 13, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618348706 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 Building ZINC001618348706 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348706 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 724) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348706 none CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 10, 5, 10, 10, 5, 6, 12, 12, 12, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 5, 10, 10, 10, 10, 10, 5, 12, 12, 12, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 725) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1) `ZINC001618348706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001618348706 none CCN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)[C@H](C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 5, 13, 13, 13, 19, 21, 21, 19, 19, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 6, 9, 9, 7, 9, 9, 6, 13, 13, 13, 19, 19, 21, 21, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618348706 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618348706 Building ZINC001618361797 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618361797 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/726 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618361797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618361797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001618361797 none O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 3, 5, 30, 33, 33, 33, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 3, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/727 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618361797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618361797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001618361797 none O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 30, 32, 32, 32, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 3, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618361797 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 Building ZINC001618361797 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618361797 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 726) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618361797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618361797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001618361797 none O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 3, 5, 30, 33, 33, 33, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 3, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 727) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618361797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618361797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001618361797 none O=C(Nc1ccc(OC(F)(F)F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 30, 32, 32, 32, 5, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 3, 5, 5, 5, 8, 8] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618361797 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618361797 Building ZINC001618462684 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618462684 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/728 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/728' -> `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)N1Cc2cccc(Cl)c2C1) `ZINC001618462684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618462684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001618462684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/729 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/729' -> `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)N1Cc2cccc(Cl)c2C1) `ZINC001618462684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618462684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001618462684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618462684 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 Building ZINC001618462684 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618462684 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 728) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1) `ZINC001618462684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618462684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001618462684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 729) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1) `ZINC001618462684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618462684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001618462684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2cccc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 29, 29, 3, 29, 29, 29, 29, 29, 29, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 29, 29, 3, 29, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618462684 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618462684 Building ZINC001618501521 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618501521 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/730 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)c(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001618501521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618501521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618501521 none O=C(N1CCc2ccc(F)c(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 46 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/731 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)c(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001618501521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618501521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618501521 none O=C(N1CCc2ccc(F)c(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 47 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618501521 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 Building ZINC001618501521 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618501521 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 730) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2ccc(F)c(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001618501521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618501521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618501521 none O=C(N1CCc2ccc(F)c(Br)c2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 46 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 731) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCc2ccc(F)c(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001618501521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618501521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618501521 none O=C(N1CCc2ccc(F)c(Br)c2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 6, 1, 6] 47 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618501521 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618501521 Building ZINC001618529982 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618529982 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/732 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1) `ZINC001618529982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618529982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001618529982 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 21, 21, 8, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/733 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1) `ZINC001618529982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618529982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001618529982 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 10, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 21, 21, 11, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618529982 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 Building ZINC001618529982 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618529982 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 732) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1) `ZINC001618529982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618529982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001618529982 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 21, 21, 8, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 733) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1) `ZINC001618529982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618529982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001618529982 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 4, 4, 21, 21, 10, 21, 21, 21, 10, 10, 10, 10, 10, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 21, 21, 11, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618529982 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618529982 Building ZINC001618691142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618691142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/734 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001618691142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618691142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618691142 none O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 25, 11, 16, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/735 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001618691142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618691142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618691142 none O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 25, 4, 4, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618691142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 Building ZINC001618691142 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618691142 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 734) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001618691142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618691142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618691142 none O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 25, 11, 16, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 735) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001618691142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618691142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001618691142 none O=C(Nc1ccc(Br)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 25, 4, 4, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 25, 25, 25, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618691142 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618691142 Building ZINC001618718725 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618718725 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/736 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(C)cc2)cn1) `ZINC001618718725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618718725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001618718725 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 3, 4, 4, 4, 4, 14, 16, 16, 15, 16, 16, 16, 6, 6, 11, 11, 11, 11, 11, 6, 2, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 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, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/737 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(C)cc2)cn1) `ZINC001618718725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618718725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001618718725 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 5, 5, 3, 5, 5, 5, 5, 15, 16, 16, 16, 16, 16, 16, 6, 6, 10, 10, 10, 10, 10, 6, 2, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 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, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618718725 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 Building ZINC001618718725 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618718725 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 736) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(C)cc2)cn1) `ZINC001618718725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618718725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001618718725 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 3, 4, 4, 4, 4, 14, 16, 16, 15, 16, 16, 16, 6, 6, 11, 11, 11, 11, 11, 6, 2, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 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, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 737) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(C)cc2)cn1) `ZINC001618718725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618718725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001618718725 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2Oc2ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 1, 8, 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, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 5, 5, 3, 5, 5, 5, 5, 15, 16, 16, 16, 16, 16, 16, 6, 6, 10, 10, 10, 10, 10, 6, 2, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 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, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618718725 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618718725 Building ZINC001618779218 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618779218 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/738 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12) `ZINC001618779218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618779218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618779218 none Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12 NO_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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 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, 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] 0 hydrogens 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, 37, 37, 31, 37, 37, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 37, 37, 31, 37, 37, 31, 6, 6, 1, 6, 31] 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, 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/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/739 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12) `ZINC001618779218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618779218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618779218 none Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12 NO_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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 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, 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] 0 hydrogens 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, 37, 37, 31, 37, 37, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 31, 31, 31, 31, 31, 37, 37, 31, 37, 37, 31, 6, 5, 1, 5, 31] 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, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618779218 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 Building ZINC001618779218 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618779218 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 738) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12) `ZINC001618779218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618779218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618779218 none Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12 NO_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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 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, 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] 0 hydrogens 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, 37, 37, 31, 37, 37, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 31, 31, 31, 31, 31, 37, 37, 31, 37, 37, 31, 6, 6, 1, 6, 31] 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, 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/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 739) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12) `ZINC001618779218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618779218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001618779218 none Cc1nn(c2ccccc2)c2ncc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc12 NO_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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 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, 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] 0 hydrogens 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, 37, 37, 31, 37, 37, 31, 31, 31, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 31, 31, 31, 31, 31, 37, 37, 31, 37, 37, 31, 6, 5, 1, 5, 31] 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, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001618779218 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001618779218 Building ZINC001626228773 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626228773 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/740 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626228773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228773 none C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 3, 5, 5, 5, 5, 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, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/741 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626228773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228773 none C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 15, 3, 5, 5, 5, 5, 15] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626228773 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 Building ZINC001626228773 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626228773 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 740) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626228773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228773 none C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 3, 5, 5, 5, 5, 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, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 741) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626228773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228773 none C[C@@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 15, 3, 5, 5, 5, 5, 15] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626228773 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228773 Building ZINC001626228774 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626228774 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/742 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626228774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228774 none C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 3, 5, 5, 5, 5, 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, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/743 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626228774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228774 none C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 17, 27, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 3, 5, 5, 5, 5, 17] 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626228774 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 Building ZINC001626228774 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626228774 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 742) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626228774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228774 none C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 16, 26, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 3, 5, 5, 5, 5, 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, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 743) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl) `ZINC001626228774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626228774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626228774 none C[C@H]1CCCCN1C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 17, 27, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 3, 5, 5, 5, 5, 17] 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626228774 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626228774 Building ZINC001621377979 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621377979 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/744 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1) `ZINC001621377979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621377979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377979 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 31, 31, 36, 36, 31, 36, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/745 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1) `ZINC001621377979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621377979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377979 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 30, 30, 41, 41, 36, 41, 41, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 41, 41, 36, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001621377979 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 Building ZINC001621377979 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621377979 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 744) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1) `ZINC001621377979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621377979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377979 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 31, 31, 36, 36, 31, 36, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 745) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1) `ZINC001621377979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621377979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377979 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 30, 30, 41, 41, 36, 41, 41, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 41, 41, 36, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001621377979 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377979 Building ZINC001621377980 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621377980 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/746 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1) `ZINC001621377980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621377980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377980 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 15, 39, 39, 47, 47, 39, 47, 47, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 47, 47, 46, 47, 47] 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]) total number of confs: 193 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/747 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1) `ZINC001621377980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621377980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377980 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 2, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 31, 31, 37, 37, 31, 37, 37, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 37, 37, 33, 37, 37] 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]) total number of confs: 141 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001621377980 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 Building ZINC001621377980 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621377980 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 746) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1) `ZINC001621377980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621377980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377980 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 15, 39, 39, 47, 47, 39, 47, 47, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 47, 47, 46, 47, 47] 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]) total number of confs: 193 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 747) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1) `ZINC001621377980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621377980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001621377980 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1CC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 6, 6, 2, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 31, 31, 37, 37, 31, 37, 37, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 37, 37, 33, 37, 37] 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]) total number of confs: 141 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001621377980 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001621377980 Building ZINC001622132249 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001622132249 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/748 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/749 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/750 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/750' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/751 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/751' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001622132249 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 Building ZINC001622132249 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001622132249 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 748) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 749) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 750) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 751) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001622132249 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 Building ZINC001622132249 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001622132249 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 748) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 749) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 750) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 751) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001622132249 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 Building ZINC001622132249 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001622132249 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 748) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 749) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 33, 38, 39, 19, 19, 13, 19, 17, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 43, 43, 39, 39, 39, 39, 39, 33, 33, 16, 19, 19, 7, 7, 2, 2, 2, 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, 47, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 750) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 751) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001622132249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001622132249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001622132249 none CCCCN(CC)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', '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', 'C.2', 'Br', 'S.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, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 38, 31, 38, 38, 17, 17, 11, 17, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 43, 43, 38, 38, 38, 38, 38, 31, 31, 13, 17, 17, 7, 7, 2, 2, 2, 17] 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: 229 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001622132249 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001622132249 Building ZINC001623327534 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623327534 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/752 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1) `ZINC001623327534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623327534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001623327534 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 9, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 3, 5, 5, 5, 5, 9, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/753 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1) `ZINC001623327534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623327534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001623327534 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 9, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 3, 5, 5, 5, 5, 9, 31, 31, 17, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623327534 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 Building ZINC001623327534 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623327534 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 752) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1) `ZINC001623327534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623327534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001623327534 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 9, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 3, 5, 5, 5, 5, 9, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 753) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1) `ZINC001623327534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623327534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001623327534 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cnn1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 9, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 17, 3, 5, 5, 5, 5, 9, 31, 31, 17, 31] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623327534 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623327534 Building ZINC001623409292 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409292 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/754 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/755 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/756 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/756' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/757 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/757' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409292 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 Building ZINC001623409292 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409292 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 754) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 755) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 756) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 757) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409292 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 Building ZINC001623409292 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409292 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 754) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 755) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 756) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 757) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409292 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 Building ZINC001623409292 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409292 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 754) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 755) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 756) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 757) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409292.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409292 none O=C(NC[C@@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 49, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409292 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409292 Building ZINC001623409298 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409298 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/758 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/759 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/760 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/760' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/761 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/761' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409298 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 Building ZINC001623409298 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409298 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 758) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 759) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 760) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 761) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409298 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 Building ZINC001623409298 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409298 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 758) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 759) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 760) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 761) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409298 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 Building ZINC001623409298 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623409298 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 758) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 759) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 37, 37, 37, 37, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 37, 37, 49, 49, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 760) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 761) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623409298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623409298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623409298 none O=C(NC[C@H]1CN(Cc2ccccc2)CC12CCC2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 11, 11, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623409298 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623409298 Building ZINC001623539392 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623539392 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/762 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623539392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623539392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623539392 none O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 17, 17, 50, 50, 50, 50, 50, 17, 2, 2] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/763 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623539392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623539392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623539392 none O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 17, 17, 50, 50, 50, 50, 50, 17, 2, 2] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623539392 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 Building ZINC001623539392 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623539392 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 762) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623539392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623539392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623539392 none O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 17, 17, 50, 50, 50, 50, 50, 17, 2, 2] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 763) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623539392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623539392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623539392 none O=C(NCc1ccc(n2cnc3ccccc32)cc1Cl)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 17, 17, 50, 50, 50, 50, 50, 17, 2, 2] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623539392 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623539392 Building ZINC001623608812 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623608812 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/764 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623608812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623608812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001623608812 none O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 32, 41, 41, 41, 37, 41, 41, 41, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 41, 41, 41, 8, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/765 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623608812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623608812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001623608812 none O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 32, 41, 41, 41, 36, 41, 41, 41, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 41, 36, 41, 8, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623608812 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 Building ZINC001623608812 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623608812 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 764) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623608812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623608812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001623608812 none O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 32, 41, 41, 41, 37, 41, 41, 41, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 41, 41, 41, 8, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 765) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623608812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623608812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001623608812 none O=C(Nc1ccc(Oc2cc(F)cc(F)c2)nc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 8, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 32, 41, 41, 41, 36, 41, 41, 41, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 2, 8, 8, 41, 36, 41, 8, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623608812 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623608812 Building ZINC001623614073 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623614073 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/766 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623614073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623614073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623614073 none O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 27, 38, 38, 35, 38, 38, 38, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 27, 27, 38, 38, 38, 38, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/767 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623614073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623614073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623614073 none O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 33, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 33, 33, 34, 34, 34, 34, 4, 4, 4, 4, 3, 3] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623614073 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 Building ZINC001623614073 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623614073 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 766) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623614073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623614073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623614073 none O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 27, 38, 38, 35, 38, 38, 38, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 27, 27, 38, 38, 38, 38, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 767) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001623614073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623614073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623614073 none O=C(N1CCC(OCc2ccc(Br)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 33, 34, 34, 34, 34, 34, 34, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 33, 33, 34, 34, 34, 34, 4, 4, 4, 4, 3, 3] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623614073 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623614073 Building ZINC001623689957 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623689957 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/768 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/768' -> `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(CCc2ccc(C)cc2)CC1) `ZINC001623689957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623689957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001623689957 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 20, 24, 26, 26, 26, 26, 26, 26, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 20, 20, 24, 24, 26, 26, 26, 26, 26, 26, 26, 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 117 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/769 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/769' -> `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(CCc2ccc(C)cc2)CC1) `ZINC001623689957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623689957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001623689957 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 18, 21, 25, 25, 24, 25, 25, 25, 6, 6, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 18, 18, 21, 21, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623689957 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 Building ZINC001623689957 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623689957 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 768) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1) `ZINC001623689957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623689957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001623689957 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 20, 24, 26, 26, 26, 26, 26, 26, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 20, 20, 24, 24, 26, 26, 26, 26, 26, 26, 26, 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 117 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 769) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1) `ZINC001623689957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623689957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001623689957 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCc2ccc(C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 18, 21, 25, 25, 24, 25, 25, 25, 6, 6, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 18, 18, 21, 21, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623689957 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623689957 Building ZINC001623722094 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623722094 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/770 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1c2ccccc2c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623722094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623722094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623722094 none O=C(NCCn1c2ccccc2c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 24, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/771 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1c2ccccc2c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623722094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623722094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623722094 none O=C(NCCn1c2ccccc2c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 5, 24, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623722094 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 Building ZINC001623722094 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623722094 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 770) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1c2ccccc2c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623722094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623722094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623722094 none O=C(NCCn1c2ccccc2c2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 5, 24, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11] 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 771) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCn1c2ccccc2c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623722094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623722094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001623722094 none O=C(NCCn1c2ccccc2c2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 5, 24, 24, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623722094 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623722094 Building ZINC001623777661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623777661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/772 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br) `ZINC001623777661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623777661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623777661 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 6, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 13, 13, 13] 34 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/773 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br) `ZINC001623777661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623777661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623777661 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 14, 14, 14] 34 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623777661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 Building ZINC001623777661 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623777661 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 772) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br) `ZINC001623777661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623777661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623777661 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 6, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 13, 13, 13] 34 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 773) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br) `ZINC001623777661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623777661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623777661 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2c1cccc2Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 14, 14, 14] 34 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623777661 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623777661 Building ZINC001623792255 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623792255 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/774 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623792255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623792255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001623792255 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 6, 17, 17, 17, 42, 42, 42, 42, 42, 42, 10, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 10, 10, 42, 42, 42, 42, 42, 42, 10, 10, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/775 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623792255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623792255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001623792255 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 4, 17, 17, 17, 42, 42, 42, 42, 42, 42, 10, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 10, 10, 42, 42, 42, 42, 42, 42, 10, 10, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623792255 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 Building ZINC001623792255 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623792255 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 774) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623792255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623792255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001623792255 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 6, 17, 17, 17, 42, 42, 42, 42, 42, 42, 10, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 10, 10, 42, 42, 42, 42, 42, 42, 10, 10, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 775) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001623792255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623792255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001623792255 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 4, 17, 17, 17, 42, 42, 42, 42, 42, 42, 10, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 10, 10, 42, 42, 42, 42, 42, 42, 10, 10, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623792255 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623792255 Building ZINC001623801480 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623801480 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/776 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)s2)CCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623801480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623801480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623801480 none O=C(NCC1(c2ccc(Br)s2)CCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 32, 36, 36, 36, 36, 36, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 36, 36, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/777 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)s2)CCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623801480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623801480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623801480 none O=C(NCC1(c2ccc(Br)s2)CCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 21, 30, 33, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 33, 33, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623801480 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 Building ZINC001623801480 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623801480 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 776) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)s2)CCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623801480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623801480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623801480 none O=C(NCC1(c2ccc(Br)s2)CCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 32, 36, 36, 36, 36, 36, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 36, 36, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 777) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)s2)CCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623801480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623801480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001623801480 none O=C(NCC1(c2ccc(Br)s2)CCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 21, 30, 33, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 33, 33, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623801480 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623801480 Building ZINC001623902988 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623902988 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/778 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 24, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/779 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 4, 12, 12, 12, 12, 12, 22, 29, 29, 29, 24, 29, 29, 29, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 22, 22, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/780 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/780' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 23, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/781 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/781' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 13, 13, 13, 13, 13, 23, 30, 30, 30, 24, 30, 30, 30, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 30, 30, 30, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623902988 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 Building ZINC001623902988 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623902988 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 778) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 24, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 779) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 4, 12, 12, 12, 12, 12, 22, 29, 29, 29, 24, 29, 29, 29, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 22, 22, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 780) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 23, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 781) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 13, 13, 13, 13, 13, 23, 30, 30, 30, 24, 30, 30, 30, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 30, 30, 30, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623902988 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 Building ZINC001623902988 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623902988 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 778) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 24, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 779) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 4, 12, 12, 12, 12, 12, 22, 29, 29, 29, 24, 29, 29, 29, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 22, 22, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 780) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 23, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 781) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 13, 13, 13, 13, 13, 23, 30, 30, 30, 24, 30, 30, 30, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 30, 30, 30, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623902988 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 Building ZINC001623902988 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623902988 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 778) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 24, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 779) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 4, 12, 12, 12, 12, 12, 22, 29, 29, 29, 24, 29, 29, 29, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 22, 22, 29, 29, 29, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 780) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 13, 23, 29, 29, 29, 23, 29, 29, 29, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 29, 25, 29, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 781) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623902988.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623902988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001623902988 none O=C(N[C@H]1CC[N@@](Cc2cc(Cl)cc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 13, 13, 13, 13, 13, 23, 30, 30, 30, 24, 30, 30, 30, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 23, 23, 30, 30, 30, 13, 13, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001623902988 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001623902988 Building ZINC001624196761 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624196761 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/782 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624196761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624196761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624196761 none CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 8, 8, 8, 8, 8, 24, 42, 43, 43, 42, 43, 43, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 8, 8, 8, 8, 42, 42, 43, 43, 43, 43, 43, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/783 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624196761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624196761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624196761 none CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 8, 8, 8, 8, 8, 22, 41, 42, 42, 42, 42, 42, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 8, 8, 8, 8, 41, 41, 42, 42, 42, 42, 42, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624196761 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 Building ZINC001624196761 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624196761 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 782) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Cc1ccccc1OCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624196761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624196761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624196761 none CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 8, 8, 8, 8, 8, 24, 42, 43, 43, 42, 43, 43, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 8, 8, 8, 8, 42, 42, 43, 43, 43, 43, 43, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 783) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Cc1ccccc1OCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624196761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624196761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001624196761 none CN(Cc1ccccc1OCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 8, 8, 8, 8, 8, 8, 22, 41, 42, 42, 42, 42, 42, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 6, 6, 8, 8, 8, 8, 41, 41, 42, 42, 42, 42, 42, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624196761 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624196761 Building ZINC001624308678 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624308678 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/784 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/784' -> `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(Cc2ccccc2)ccc1O) `ZINC001624308678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624308678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001624308678 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 19, 31, 31, 19, 31, 31, 5, 6, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 6, 19, 19, 31, 31, 19, 31, 31, 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, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/785 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/785' -> `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(Cc2ccccc2)ccc1O) `ZINC001624308678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624308678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001624308678 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 34, 34, 21, 34, 34, 6, 6, 6, 6, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 6, 21, 21, 34, 34, 21, 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, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624308678 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 Building ZINC001624308678 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624308678 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 784) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)ccc1O) `ZINC001624308678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624308678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001624308678 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 19, 31, 31, 19, 31, 31, 5, 6, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 6, 19, 19, 31, 31, 19, 31, 31, 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, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 785) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)ccc1O) `ZINC001624308678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624308678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001624308678 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cc2ccccc2)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 21, 34, 34, 21, 34, 34, 6, 6, 6, 6, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 6, 21, 21, 34, 34, 21, 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, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624308678 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624308678 Building ZINC001624357612 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624357612 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/786 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1) `ZINC001624357612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624357612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357612 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 23, 23, 25, 25, 25, 25, 25, 8, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 23, 23, 23, 23, 25, 25, 25, 25, 25, 26, 26, 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, 58]) total number of confs: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/787 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1) `ZINC001624357612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624357612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357612 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 18, 19, 19, 19, 19, 19, 19, 6, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 18, 18, 19, 19, 19, 19, 19, 19, 19, 25, 25, 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, 58]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624357612 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 Building ZINC001624357612 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624357612 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 786) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1) `ZINC001624357612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624357612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357612 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 23, 23, 25, 25, 25, 25, 25, 8, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 23, 23, 23, 23, 25, 25, 25, 25, 25, 26, 26, 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, 58]) total number of confs: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 787) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1) `ZINC001624357612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624357612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357612 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 18, 19, 19, 19, 19, 19, 19, 6, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 18, 18, 19, 19, 19, 19, 19, 19, 19, 25, 25, 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, 58]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624357612 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357612 Building ZINC001624357613 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624357613 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/788 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1) `ZINC001624357613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624357613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357613 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 20, 22, 22, 22, 22, 22, 22, 6, 24, 24, 24, 24, 24, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 20, 20, 22, 22, 22, 22, 22, 22, 22, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/789 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1) `ZINC001624357613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624357613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357613 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 23, 23, 25, 25, 24, 25, 25, 8, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 5, 23, 23, 23, 23, 25, 25, 25, 25, 25, 26, 26, 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, 58]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624357613 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 Building ZINC001624357613 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624357613 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 788) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1) `ZINC001624357613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624357613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357613 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 20, 22, 22, 22, 22, 22, 22, 6, 24, 24, 24, 24, 24, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 20, 20, 22, 22, 22, 22, 22, 22, 22, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 789) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1) `ZINC001624357613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624357613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624357613 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCc1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 8, 8, 23, 23, 25, 25, 24, 25, 25, 8, 26, 26, 26, 26, 26, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 5, 23, 23, 23, 23, 25, 25, 25, 25, 25, 26, 26, 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, 58]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624357613 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624357613 Building ZINC001624397834 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624397834 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/790 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624397834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397834 none COc1ccc(C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 20, 20, 12, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 7, 7, 15, 9, 9, 20, 20, 20, 20, 20, 20, 20, 12, 12, 4, 7, 7, 7, 7, 9, 9, 15, 15, 15, 9, 9, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/791 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624397834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397834 none COc1ccc(C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 12, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 8, 12, 8, 8, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 6, 6, 6, 6, 8, 8, 12, 12, 12, 8, 8, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624397834 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 Building ZINC001624397834 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624397834 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 790) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624397834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397834 none COc1ccc(C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 20, 20, 12, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 7, 7, 15, 9, 9, 20, 20, 20, 20, 20, 20, 20, 12, 12, 4, 7, 7, 7, 7, 9, 9, 15, 15, 15, 9, 9, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 791) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624397834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397834 none COc1ccc(C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 12, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 8, 12, 8, 8, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 6, 6, 6, 6, 8, 8, 12, 12, 12, 8, 8, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624397834 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624397834 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397834 Building ZINC001624397835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624397835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/792 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624397835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397835 none COc1ccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 6, 12, 8, 8, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 6, 6, 6, 6, 8, 8, 12, 12, 12, 8, 8, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/793 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624397835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397835 none COc1ccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 7, 7, 15, 9, 9, 19, 19, 19, 19, 19, 19, 19, 12, 12, 4, 7, 7, 7, 7, 9, 9, 15, 15, 15, 9, 9, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624397835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 Building ZINC001624397835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624397835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 792) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624397835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397835 none COc1ccc(C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 6, 12, 8, 8, 17, 17, 17, 17, 17, 17, 17, 12, 12, 3, 6, 6, 6, 6, 8, 8, 12, 12, 12, 8, 8, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 793) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1) `ZINC001624397835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624397835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001624397835 none COc1ccc(C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 7, 7, 15, 9, 9, 19, 19, 19, 19, 19, 19, 19, 12, 12, 4, 7, 7, 7, 7, 9, 9, 15, 15, 15, 9, 9, 19, 19] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624397835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624397835 Building ZINC001624430498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624430498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/794 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624430498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430498 none C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 27, 27, 14, 14, 27, 27, 27, 27, 27, 14, 14, 14, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 16, 16, 8, 14, 14, 14, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 8, 16, 16, 8, 16, 16, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/795 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624430498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430498 none C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 25, 25, 13, 13, 25, 25, 25, 25, 25, 13, 13, 13, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 9, 15, 15, 9, 15, 15, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624430498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 Building ZINC001624430498 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624430498 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 794) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624430498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430498 none C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 27, 27, 14, 14, 27, 27, 27, 27, 27, 14, 14, 14, 7, 1, 7, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 16, 16, 8, 14, 14, 14, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 8, 16, 16, 8, 16, 16, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 795) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624430498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430498 none C[C@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 25, 25, 13, 13, 25, 25, 25, 25, 25, 13, 13, 13, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 9, 15, 15, 9, 15, 15, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624430498 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430498 Building ZINC001624430499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624430499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/796 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624430499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430499 none C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 24, 24, 13, 13, 24, 24, 24, 24, 24, 13, 13, 13, 5, 1, 7, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 13, 13, 13, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 9, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/797 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624430499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430499 none C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 28, 28, 15, 15, 28, 28, 28, 28, 28, 15, 15, 15, 5, 1, 8, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 15, 15, 15, 28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 6, 14, 14, 6, 14, 14, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624430499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 Building ZINC001624430499 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624430499 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 796) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624430499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430499 none C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 24, 24, 13, 13, 24, 24, 24, 24, 24, 13, 13, 13, 5, 1, 7, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 13, 13, 13, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 9, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 797) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624430499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624430499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001624430499 none C[C@@]1(c2ccc(C(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 28, 28, 15, 15, 28, 28, 28, 28, 28, 15, 15, 15, 5, 1, 8, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 15, 15, 15, 28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 6, 14, 14, 6, 14, 14, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624430499 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624430499 Building ZINC001624432669 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624432669 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/798 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)CC2)c1) `ZINC001624432669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624432669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624432669 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)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.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 17, 17, 17, 17, 28, 28, 27, 28, 28, 28, 17, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 8, 8, 17, 17, 28, 28, 28, 28, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/799 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)CC2)c1) `ZINC001624432669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624432669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624432669 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)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.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 11, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 18, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 11, 11, 18, 18, 27, 27, 27, 27, 6, 6, 6, 6, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624432669 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 Building ZINC001624432669 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624432669 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 798) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)CC2)c1) `ZINC001624432669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624432669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624432669 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)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.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 17, 17, 17, 17, 28, 28, 27, 28, 28, 28, 17, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 8, 8, 17, 17, 28, 28, 28, 28, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 799) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)CC2)c1) `ZINC001624432669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624432669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624432669 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3ccc(c4ccccc4Cl)s3)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.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 11, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 18, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 11, 11, 18, 18, 27, 27, 27, 27, 6, 6, 6, 6, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624432669 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624432669 Building ZINC001624536440 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624536440 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/800 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccnc3ccccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624536440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624536440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001624536440 none O=C(N1CCC(c2ccnc3ccccc32)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 10, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/801 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccnc3ccccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624536440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624536440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001624536440 none O=C(N1CCC(c2ccnc3ccccc32)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624536440 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 Building ZINC001624536440 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624536440 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 800) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC(c2ccnc3ccccc32)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624536440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624536440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001624536440 none O=C(N1CCC(c2ccnc3ccccc32)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 10, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 59 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 801) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCC(c2ccnc3ccccc32)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001624536440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624536440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001624536440 none O=C(N1CCC(c2ccnc3ccccc32)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 10, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 64 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624536440 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624536440 Building ZINC001624588654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624588654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/802 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001624588654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624588654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624588654 none NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 40, 40, 37, 40, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 19, 33, 33, 40, 40, 40, 40, 40, 4, 3, 1, 3, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/803 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001624588654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624588654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624588654 none NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 18, 32, 40, 40, 35, 40, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 18, 32, 32, 40, 40, 40, 40, 40, 4, 3, 1, 3, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624588654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 Building ZINC001624588654 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624588654 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 802) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001624588654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624588654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624588654 none NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 40, 40, 37, 40, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 19, 33, 33, 40, 40, 40, 40, 40, 4, 3, 1, 3, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 803) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001624588654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624588654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624588654 none NC(=O)c1ccc(NCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 18, 32, 40, 40, 35, 40, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 18, 32, 32, 40, 40, 40, 40, 40, 4, 3, 1, 3, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624588654 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624588654 Building ZINC001624630170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624630170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/804 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001624630170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624630170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001624630170 none Cc1nc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 44, 27, 27, 27, 27, 13, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 44, 44, 44, 44, 44, 27, 27, 13, 13, 8, 8, 2, 5, 5, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/805 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001624630170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624630170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001624630170 none Cc1nc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 44, 27, 27, 27, 27, 13, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 27, 44, 44, 44, 44, 44, 27, 27, 13, 13, 8, 8, 2, 6, 6, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624630170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 Building ZINC001624630170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624630170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 804) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001624630170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624630170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001624630170 none Cc1nc(c2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 44, 27, 27, 27, 27, 13, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 44, 44, 44, 44, 44, 27, 27, 13, 13, 8, 8, 2, 5, 5, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 805) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1) `ZINC001624630170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624630170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001624630170 none Cc1nc(c2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 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: [44, 44, 44, 27, 27, 27, 27, 13, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 27, 44, 44, 44, 44, 44, 27, 27, 13, 13, 8, 8, 2, 6, 6, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624630170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624630170 Building ZINC001624705799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/806 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/807 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/808 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/808' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/809 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/809' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 Building ZINC001624705799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 806) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 807) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 808) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 809) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 Building ZINC001624705799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 806) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 807) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 808) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 809) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 Building ZINC001624705799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 806) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 807) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 808) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 25, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 25, 25, 25, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 809) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705799.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705799 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 5, 8, 8, 10, 10, 8, 10, 16, 10, 10, 9, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 5, 5, 10, 10, 16, 16, 16, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705799 Building ZINC001624705800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/810 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/811 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/812 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/812' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/813 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/813' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 Building ZINC001624705800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 810) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 811) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 812) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 813) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 Building ZINC001624705800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 810) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 811) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 812) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 813) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 Building ZINC001624705800 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624705800 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 810) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 811) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 812) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 6, 9, 9, 11, 11, 11, 11, 17, 11, 11, 10, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 11, 11, 17, 17, 17, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 813) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1) `ZINC001624705800.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624705800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624705800 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](c1ccc(SC)cc1)N1CCc2sccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 14, 5, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 7, 11, 11, 11, 11, 11, 11, 23, 11, 11, 12, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 7, 7, 11, 11, 23, 23, 23, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624705800 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624705800 Building ZINC001624905791 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624905791 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/814 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624905791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905791 none O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 7, 7, 6, 6, 31, 34, 34, 7, 7, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 34, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/815 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624905791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905791 none O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 8, 6, 6, 31, 35, 35, 8, 8, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 35, 8, 8, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624905791 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 Building ZINC001624905791 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624905791 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 814) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624905791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905791 none O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 7, 7, 6, 6, 31, 34, 34, 7, 7, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 34, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 815) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624905791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905791 none O=C(N[C@@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 8, 6, 6, 31, 35, 35, 8, 8, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 35, 8, 8, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624905791 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905791 Building ZINC001624905792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624905792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/816 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624905792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905792 none O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 8, 6, 6, 31, 35, 35, 8, 8, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 35, 8, 8, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/817 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624905792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905792 none O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 7, 7, 6, 6, 30, 33, 33, 7, 7, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 33, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624905792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 Building ZINC001624905792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624905792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 816) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624905792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905792 none O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 8, 8, 6, 6, 31, 35, 35, 8, 8, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 35, 8, 8, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 817) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624905792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624905792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001624905792 none O=C(N[C@H](c1ccc(OC(F)F)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 7, 7, 6, 6, 30, 33, 33, 7, 7, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 33, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624905792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624905792 Building ZINC001624914867 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624914867 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/818 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001624914867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624914867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624914867 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 17, 17, 17, 13, 10, 10, 10, 10, 10, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 30, 30, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 7, 7, 3, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/819 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001624914867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624914867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624914867 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 14, 11, 11, 11, 11, 11, 11, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 31, 31, 31, 19, 19, 11, 11, 11, 8, 8, 3, 4, 4, 4, 4, 19, 19] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624914867 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 Building ZINC001624914867 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624914867 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 818) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001624914867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624914867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624914867 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 17, 17, 17, 13, 10, 10, 10, 10, 10, 10, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 30, 30, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 7, 7, 3, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 819) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001624914867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624914867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624914867 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 14, 11, 11, 11, 11, 11, 11, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 31, 31, 31, 31, 31, 31, 31, 19, 19, 11, 11, 11, 8, 8, 3, 4, 4, 4, 4, 19, 19] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624914867 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624914867 Building ZINC001624934740 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624934740 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/820 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1) `ZINC001624934740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624934740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001624934740 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 28, 28, 28, 15, 15, 3, 6, 6, 15, 31, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/821 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1) `ZINC001624934740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624934740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001624934740 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 29, 29, 29, 15, 15, 3, 6, 6, 15, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624934740 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 Building ZINC001624934740 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624934740 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 820) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1) `ZINC001624934740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624934740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001624934740 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 28, 28, 28, 15, 15, 3, 6, 6, 15, 31, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 821) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1) `ZINC001624934740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624934740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001624934740 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1C(=O)c1ccccc1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 29, 29, 29, 15, 15, 3, 6, 6, 15, 31, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624934740 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624934740 Building ZINC001624940437 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624940437 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/822 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624940437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940437 none COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 23, 23, 23, 23, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 27, 27, 27, 27, 23, 23, 23, 9, 9, 3, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/823 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624940437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940437 none COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 25, 25, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 26, 28, 28, 28, 25, 25, 25, 9, 9, 2, 4, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624940437 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 Building ZINC001624940437 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624940437 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 822) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624940437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940437 none COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 23, 23, 23, 23, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 27, 27, 27, 27, 23, 23, 23, 9, 9, 3, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 823) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624940437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940437 none COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 25, 25, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 26, 28, 28, 28, 25, 25, 25, 9, 9, 2, 4, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/11891/xbl-8058088.38/working/building/ZINC001624940437 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624940437 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940437 Building ZINC001624940438 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624940438 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/824 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624940438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940438 none COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 25, 25, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 26, 28, 28, 28, 25, 25, 25, 9, 9, 2, 4, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/825 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624940438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940438 none COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 23, 23, 23, 23, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 27, 27, 27, 27, 23, 23, 23, 9, 9, 3, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624940438 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 Building ZINC001624940438 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624940438 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 824) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624940438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940438 none COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 25, 25, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 25, 26, 28, 28, 28, 25, 25, 25, 9, 9, 2, 4, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 825) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC) `ZINC001624940438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624940438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001624940438 none COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c2c[nH]c3ccccc32)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 23, 23, 23, 23, 21, 9, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 23, 27, 27, 27, 27, 23, 23, 23, 9, 9, 3, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 26, 26, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/11891/xbl-8058088.38/working/building/ZINC001624940438 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624940438 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624940438 Building ZINC001624942462 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624942462 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/826 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624942462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942462 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 19, 20, 31, 31, 31, 11, 11, 11, 6, 3, 3, 3, 2, 3, 3, 3, 3, 6, 6, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/827 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624942462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942462 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 16, 17, 28, 28, 28, 9, 9, 9, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 4, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624942462 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 Building ZINC001624942462 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624942462 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 826) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624942462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942462 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 19, 20, 31, 31, 31, 11, 11, 11, 6, 3, 3, 3, 2, 3, 3, 3, 3, 6, 6, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 827) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624942462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942462 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 16, 17, 28, 28, 28, 9, 9, 9, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 4, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624942462 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942462 Building ZINC001624942463 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624942463 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/828 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624942463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942463 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 28, 28, 28, 9, 9, 9, 5, 3, 3, 3, 2, 2, 2, 2, 2, 5, 5, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/829 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624942463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942463 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 18, 18, 29, 29, 29, 10, 10, 10, 6, 3, 3, 3, 2, 3, 3, 3, 3, 6, 6, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624942463 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 Building ZINC001624942463 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624942463 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 828) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624942463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942463 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 17, 28, 28, 28, 9, 9, 9, 5, 3, 3, 3, 2, 2, 2, 2, 2, 5, 5, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 829) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCCC(C)C) `ZINC001624942463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624942463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001624942463 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 18, 18, 29, 29, 29, 10, 10, 10, 6, 3, 3, 3, 2, 3, 3, 3, 3, 6, 6, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624942463 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624942463 Building ZINC001624944489 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624944489 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/830 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccco1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001624944489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624944489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001624944489 none O=C(NCc1ccco1)Nc1ccc(NC(=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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 17, 42, 42, 50, 50, 50, 17, 8, 8, 2, 2, 1, 2, 8, 8] 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, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/831 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccco1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001624944489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624944489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001624944489 none O=C(NCc1ccco1)Nc1ccc(NC(=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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 17, 42, 42, 50, 50, 50, 17, 8, 8, 2, 2, 1, 2, 8, 8] 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, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624944489 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 Building ZINC001624944489 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624944489 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 830) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccco1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001624944489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624944489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001624944489 none O=C(NCc1ccco1)Nc1ccc(NC(=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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 17, 42, 42, 50, 50, 50, 17, 8, 8, 2, 2, 1, 2, 8, 8] 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, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 831) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccco1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001624944489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624944489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001624944489 none O=C(NCc1ccco1)Nc1ccc(NC(=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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 17, 42, 42, 50, 50, 50, 17, 8, 8, 2, 2, 1, 2, 8, 8] 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, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624944489 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624944489 Building ZINC001624954458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624954458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/832 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624954458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624954458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624954458 none O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 15, 16, 16, 16, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 15, 15, 16, 16, 16, 16, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/833 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624954458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624954458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624954458 none O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 5, 16, 17, 17, 17, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 16, 16, 17, 17, 17, 17, 31, 31, 31, 31, 31, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624954458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 Building ZINC001624954458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624954458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 832) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624954458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624954458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624954458 none O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 15, 16, 16, 16, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 15, 15, 16, 16, 16, 16, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 833) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624954458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624954458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624954458 none O=C(Nc1cccc(COCCOc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 5, 16, 17, 17, 17, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 16, 16, 17, 17, 17, 17, 31, 31, 31, 31, 31, 5, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624954458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624954458 Building ZINC001624976674 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624976674 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/834 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624976674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624976674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624976674 none CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 19, 19, 19, 15, 19, 19, 15, 13, 13, 13, 13, 13, 13, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 34, 34, 19, 19, 19, 19, 13, 13, 13, 11, 11, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/835 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624976674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624976674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624976674 none CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 19, 19, 19, 15, 19, 19, 15, 12, 12, 12, 12, 12, 12, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 34, 34, 19, 19, 19, 19, 12, 12, 12, 10, 10, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624976674 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 Building ZINC001624976674 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624976674 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 834) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624976674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624976674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624976674 none CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 19, 19, 19, 15, 19, 19, 15, 13, 13, 13, 13, 13, 13, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 34, 34, 19, 19, 19, 19, 13, 13, 13, 11, 11, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 835) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624976674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624976674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001624976674 none CCCOc1ccccc1Oc1ncccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 19, 19, 19, 15, 19, 19, 15, 12, 12, 12, 12, 12, 12, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 34, 34, 19, 19, 19, 19, 12, 12, 12, 10, 10, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001624976674 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001624976674 Building ZINC001625061186 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625061186 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/836 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001625061186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625061186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625061186 none CC(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 2, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 10, 10, 10, 5, 5, 2, 2, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/837 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001625061186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625061186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625061186 none CC(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 2, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 10, 11, 10, 5, 5, 2, 2, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625061186 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 Building ZINC001625061186 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625061186 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 836) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001625061186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625061186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625061186 none CC(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 2, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 10, 10, 10, 5, 5, 2, 2, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 837) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001625061186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625061186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625061186 none CC(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 2, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 10, 11, 10, 5, 5, 2, 2, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625061186 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625061186 Building ZINC001625078758 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625078758 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/838 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1) `ZINC001625078758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625078758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001625078758 none COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 3, 3, 8, 50, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/839 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1) `ZINC001625078758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625078758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001625078758 none COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 3, 3, 8, 50, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625078758 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 Building ZINC001625078758 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625078758 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 838) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1) `ZINC001625078758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625078758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001625078758 none COc1ccc(Cc2nc3ccc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 3, 3, 8, 50, 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: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 839) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1) `ZINC001625078758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625078758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001625078758 none COc1ccc(Cc2nc3ccc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)cc3[nH]2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 3, 3, 8, 50, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625078758 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625078758 Building ZINC001625200991 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625200991 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/840 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625200991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200991 none CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 6, 14, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 19, 19, 15, 19, 19, 19, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 6, 8, 8, 8, 8, 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]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/841 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625200991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200991 none CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 6, 13, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 20, 20, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 6, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625200991 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 Building ZINC001625200991 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625200991 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 840) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625200991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200991 none CC(C)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 6, 14, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 19, 19, 15, 19, 19, 19, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 6, 8, 8, 8, 8, 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]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 841) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625200991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200991 none CC(C)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 6, 13, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 20, 20, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 6, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625200991 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200991 Building ZINC001625200992 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625200992 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/842 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625200992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200992 none CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 6, 13, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 20, 20, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 6, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/843 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625200992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200992 none CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 6, 14, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 19, 19, 18, 18, 19, 19, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 6, 8, 8, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625200992 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 Building ZINC001625200992 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625200992 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 842) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625200992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200992 none CC(C)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 20, 6, 13, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 20, 20, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 6, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 843) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1) `ZINC001625200992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625200992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625200992 none CC(C)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 6, 14, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 19, 19, 18, 18, 19, 19, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 6, 8, 8, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625200992 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625200992 Building ZINC001625256170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625256170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/844 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/844' -> `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]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625256170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256170 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 8, 8, 6, 6, 19, 19, 19, 23, 23, 19, 20, 23, 23, 8, 8, 6, 6, 6, 3, 4, 4, 4, 4, 8, 8, 19, 23, 23, 23, 23, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/845 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/845' -> `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]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625256170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256170 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 6, 6, 25, 25, 25, 33, 33, 25, 28, 33, 33, 10, 10, 6, 6, 6, 3, 6, 6, 6, 6, 10, 10, 25, 33, 33, 33, 33, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625256170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 Building ZINC001625256170 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625256170 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 844) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625256170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256170 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 8, 8, 6, 6, 19, 19, 19, 23, 23, 19, 20, 23, 23, 8, 8, 6, 6, 6, 3, 4, 4, 4, 4, 8, 8, 19, 23, 23, 23, 23, 8, 8] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 845) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625256170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256170 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 6, 6, 25, 25, 25, 33, 33, 25, 28, 33, 33, 10, 10, 6, 6, 6, 3, 6, 6, 6, 6, 10, 10, 25, 33, 33, 33, 33, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625256170 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256170 Building ZINC001625256171 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625256171 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/846 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/846' -> `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]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625256171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256171 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 11, 11, 7, 7, 23, 23, 23, 31, 31, 23, 23, 31, 31, 11, 11, 7, 7, 7, 4, 6, 6, 6, 6, 11, 11, 23, 31, 31, 31, 31, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/847 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/847' -> `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]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625256171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256171 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 6, 6, 21, 21, 21, 26, 26, 21, 21, 26, 26, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 21, 26, 26, 26, 26, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625256171 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 Building ZINC001625256171 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625256171 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 846) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625256171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256171 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 11, 11, 7, 7, 23, 23, 23, 31, 31, 23, 23, 31, 31, 11, 11, 7, 7, 7, 4, 6, 6, 6, 6, 11, 11, 23, 31, 31, 31, 31, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 847) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(F)cc2)cc1) `ZINC001625256171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625256171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001625256171 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccc(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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 6, 6, 21, 21, 21, 26, 26, 21, 21, 26, 26, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 21, 26, 26, 26, 26, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625256171 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625256171 Building ZINC001625260851 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625260851 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/848 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F) `ZINC001625260851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625260851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001625260851 none Cc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 10, 10, 22, 27, 27, 27, 27, 18, 18, 18, 18, 10, 10, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/849 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F) `ZINC001625260851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625260851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001625260851 none Cc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 14, 16, 32, 33, 33, 33, 33, 20, 20, 20, 20, 11, 11, 5, 5, 5, 4, 4, 4, 4, 20, 20, 20, 20, 33, 33] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625260851 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 Building ZINC001625260851 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625260851 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 848) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F) `ZINC001625260851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625260851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001625260851 none Cc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 10, 10, 22, 27, 27, 27, 27, 18, 18, 18, 18, 10, 10, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 849) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F) `ZINC001625260851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625260851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001625260851 none Cc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(C)c1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 14, 16, 32, 33, 33, 33, 33, 20, 20, 20, 20, 11, 11, 5, 5, 5, 4, 4, 4, 4, 20, 20, 20, 20, 33, 33] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625260851 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625260851 Building ZINC001625306459 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625306459 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/850 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625306459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306459 none CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/851 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625306459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306459 none CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 26, 26, 26, 11, 11, 11, 11, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625306459 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 Building ZINC001625306459 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625306459 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 850) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625306459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306459 none CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 851) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625306459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306459 none CC1(C)[C@@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 26, 26, 26, 11, 11, 11, 11, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625306459 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306459 Building ZINC001625306460 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625306460 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/852 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625306460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306460 none CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 26, 26, 26, 11, 11, 11, 11, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/853 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625306460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306460 none CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625306460 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 Building ZINC001625306460 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625306460 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 852) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625306460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306460 none CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 26, 26, 26, 11, 11, 11, 11, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 853) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001625306460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625306460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001625306460 none CC1(C)[C@H](c2ccc(F)c(F)c2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625306460 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625306460 Building ZINC001625318283 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625318283 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/854 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625318283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001625318283 none O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 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] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 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, 13, 25, 25, 25, 17, 25, 25, 25, 6, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 25, 17, 25, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/855 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625318283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001625318283 none O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 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] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 14, 25, 25, 25, 17, 25, 25, 25, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 25, 17, 25, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625318283 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 Building ZINC001625318283 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625318283 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 854) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625318283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001625318283 none O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 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] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 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, 13, 25, 25, 25, 17, 25, 25, 25, 6, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 25, 17, 25, 10, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 855) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625318283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625318283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001625318283 none O=C(N(Cc1cc(Br)ccc1F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 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] dock color type numbers: [6, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 14, 25, 25, 25, 17, 25, 25, 25, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 25, 17, 25, 11, 11, 11, 11, 11, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625318283 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625318283 Building ZINC001625403707 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625403707 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/856 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C) `ZINC001625403707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625403707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001625403707 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 16, 28, 28, 29, 29, 29, 29, 16, 16, 16, 16, 16, 12, 12, 2, 6, 6, 2, 3, 3, 3, 3, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/857 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C) `ZINC001625403707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625403707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001625403707 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 13, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 16, 27, 27, 28, 28, 28, 28, 16, 16, 16, 16, 16, 13, 13, 6, 6, 6, 2, 3, 3, 3, 3, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625403707 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 Building ZINC001625403707 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625403707 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 856) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C) `ZINC001625403707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625403707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001625403707 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 16, 28, 28, 29, 29, 29, 29, 16, 16, 16, 16, 16, 12, 12, 2, 6, 6, 2, 3, 3, 3, 3, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 857) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C) `ZINC001625403707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625403707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001625403707 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 13, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 16, 27, 27, 28, 28, 28, 28, 16, 16, 16, 16, 16, 13, 13, 6, 6, 6, 2, 3, 3, 3, 3, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625403707 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625403707 Building ZINC001625411936 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625411936 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/858 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl) `ZINC001625411936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625411936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001625411936 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 18, 25, 25, 25, 25, 25, 25, 18, 18, 18, 4, 4, 4, 9, 9, 9, 4, 4, 2, 7, 7, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/859 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl) `ZINC001625411936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625411936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001625411936 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 18, 25, 25, 25, 25, 25, 25, 18, 18, 18, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625411936 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 Building ZINC001625411936 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625411936 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 858) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl) `ZINC001625411936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625411936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001625411936 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 18, 25, 25, 25, 25, 25, 25, 18, 18, 18, 4, 4, 4, 9, 9, 9, 4, 4, 2, 7, 7, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 859) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl) `ZINC001625411936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625411936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001625411936 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(Br)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 18, 25, 25, 25, 25, 25, 25, 18, 18, 18, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 25, 25, 25, 25, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625411936 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625411936 Building ZINC001625471900 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471900 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/860 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471900 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 49, 49, 49, 49, 147] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/861 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471900 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 3, 2, 3, 49, 49, 49, 49, 147] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471900 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 Building ZINC001625471900 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471900 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 860) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471900 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 49, 49, 49, 49, 147] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 861) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471900 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 3, 2, 3, 49, 49, 49, 49, 147] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471900 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471900 Building ZINC001625471902 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471902 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/862 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471902 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/863 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471902 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471902 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 Building ZINC001625471902 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471902 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 862) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471902 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 863) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471902 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471902 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471902 Building ZINC001625471904 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471904 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/864 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471904 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 276 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/865 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471904 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471904 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 Building ZINC001625471904 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471904 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 864) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471904 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 276 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 865) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001625471904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471904 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 2, 50, 50, 50, 50, 150] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471904 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471904 Building ZINC001625471905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/866 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471905 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 4, 1, 4, 48, 48, 48, 48, 144] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 285 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/867 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471905 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 4, 2, 4, 48, 48, 48, 48, 144] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 280 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 Building ZINC001625471905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625471905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 866) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625471905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471905 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 4, 1, 4, 48, 48, 48, 48, 144] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 285 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 867) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001625471905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625471905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001625471905 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 4, 2, 4, 48, 48, 48, 48, 144] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 280 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625471905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625471905 Building ZINC001625554475 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625554475 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/868 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl) `ZINC001625554475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625554475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001625554475 none CCOC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 39, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 6, 8, 8, 8, 45, 45, 45, 45, 45, 16, 16, 4, 3, 1, 3, 8, 8, 7, 8] 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/869 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl) `ZINC001625554475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625554475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001625554475 none CCOC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 38, 13, 38, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 7, 7, 5, 7, 7, 7, 45, 45, 45, 45, 45, 13, 13, 3, 3, 1, 3, 7, 7, 7, 7] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625554475 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 Building ZINC001625554475 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625554475 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 868) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl) `ZINC001625554475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625554475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001625554475 none CCOC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 39, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 6, 8, 8, 8, 45, 45, 45, 45, 45, 16, 16, 4, 3, 1, 3, 8, 8, 7, 8] 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 869) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl) `ZINC001625554475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625554475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001625554475 none CCOC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 38, 38, 13, 38, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 7, 7, 5, 7, 7, 7, 45, 45, 45, 45, 45, 13, 13, 3, 3, 1, 3, 7, 7, 7, 7] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625554475 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625554475 Building ZINC001625568819 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568819 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/870 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568819 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 34, 19, 34, 19, 19, 19, 19, 19, 19, 19, 19, 8, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 5, 5, 19, 19, 19, 19] 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: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/871 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568819 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 23, 38, 23, 23, 23, 23, 23, 23, 23, 23, 10, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 6, 6, 23, 23, 23, 23] 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: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625568819 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 Building ZINC001625568819 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568819 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 870) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568819 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 34, 19, 34, 19, 19, 19, 19, 19, 19, 19, 19, 8, 19, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 5, 5, 19, 19, 19, 19] 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: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 871) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568819 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 23, 38, 23, 23, 23, 23, 23, 23, 23, 23, 10, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 6, 6, 23, 23, 23, 23] 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: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625568819 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568819 Building ZINC001625568820 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568820 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/872 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568820 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/873 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568820 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 26, 17, 17, 17, 17, 17, 17, 17, 17, 9, 17, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 8, 8, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625568820 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 Building ZINC001625568820 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568820 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 872) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568820 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 15, 9, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 7, 7, 15, 15, 15, 15] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 873) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001625568820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001625568820 none CC(C)(C)OC(=O)N1CCC2(CCCC[C@H]2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 26, 17, 17, 17, 17, 17, 17, 17, 17, 9, 17, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 8, 8, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625568820 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625568820 Building ZINC001625725835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625725835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/874 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625725835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725835 none O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 3, 5, 5, 5, 16, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/875 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625725835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725835 none O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 3, 6, 6, 6, 18, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625725835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 Building ZINC001625725835 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625725835 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 874) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625725835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725835 none O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 3, 5, 5, 5, 16, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 875) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625725835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725835 none O=C(Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 3, 6, 6, 6, 18, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625725835 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725835 Building ZINC001625725836 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625725836 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/876 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625725836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725836 none O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 18, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/877 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625725836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725836 none O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 15, 28, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625725836 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 Building ZINC001625725836 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625725836 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 876) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625725836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725836 none O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 18, 29, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 877) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625725836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625725836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625725836 none O=C(Nc1cc(Cl)ccc1OC[C@H]1CCCCO1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 15, 28, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001625725836 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001625725836 Building ZINC001626245806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626245806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/878 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626245806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245806 none O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 22, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/879 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626245806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245806 none O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626245806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 Building ZINC001626245806 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626245806 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 878) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626245806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245806 none O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 22, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 879) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626245806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245806 none O=C(N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626245806 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245806 Building ZINC001626245808 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626245808 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/880 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626245808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245808 none O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 19, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/881 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626245808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245808 none O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626245808 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 Building ZINC001626245808 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626245808 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 880) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626245808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245808 none O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 19, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 881) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001626245808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626245808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626245808 none O=C(N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 20, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626245808 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626245808 Building ZINC001626293085 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626293085 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/882 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626293085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293085 none Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 21, 31, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/883 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626293085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293085 none Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 14, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626293085 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 Building ZINC001626293085 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626293085 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 882) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626293085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293085 none Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 21, 31, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 883) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626293085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293085 none Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 14, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626293085 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293085 Building ZINC001626293086 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626293086 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/884 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626293086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293086 none Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 12, 19, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/885 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626293086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293086 none Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 22, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626293086 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 Building ZINC001626293086 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626293086 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 884) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626293086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293086 none Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 12, 19, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 885) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Br) `ZINC001626293086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626293086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001626293086 none Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 22, 31, 31, 31, 31, 31, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626293086 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626293086 Building ZINC001626360005 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626360005 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/886 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1) `ZINC001626360005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626360005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626360005 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 44, 44, 13, 13, 44, 44, 44, 44, 44, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 44, 44, 44, 44, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/887 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1) `ZINC001626360005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626360005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626360005 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 4, 13, 13, 13, 13, 13, 48, 48, 13, 21, 48, 48, 48, 48, 48, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 13, 13, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626360005 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 Building ZINC001626360005 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626360005 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 886) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1) `ZINC001626360005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626360005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626360005 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 5, 13, 13, 13, 13, 13, 44, 44, 13, 13, 44, 44, 44, 44, 44, 13, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 13, 44, 44, 44, 44, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 887) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1) `ZINC001626360005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626360005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626360005 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 4, 13, 13, 13, 13, 13, 48, 48, 13, 21, 48, 48, 48, 48, 48, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 13, 13, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626360005 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626360005 Building ZINC001626411454 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626411454 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/888 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626411454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626411454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001626411454 none CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 7, 7, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 15, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/889 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626411454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626411454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001626411454 none CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 7, 7, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 15, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626411454 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 Building ZINC001626411454 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626411454 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 888) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626411454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626411454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001626411454 none CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 7, 7, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 15, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 889) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626411454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626411454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001626411454 none CN(CCCc1cc(c2cccc(F)c2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 6, 7, 7, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 3, 6, 6, 7, 7, 7, 7, 15, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626411454 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626411454 Building ZINC001626501006 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626501006 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/890 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl) `ZINC001626501006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626501006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626501006 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 2, 10, 10, 1, 1, 1, 2, 8, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 15, 15, 15, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/891 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl) `ZINC001626501006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626501006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626501006 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 2, 9, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626501006 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 Building ZINC001626501006 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626501006 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 890) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl) `ZINC001626501006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626501006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626501006 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 2, 10, 10, 1, 1, 1, 2, 8, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 15, 15, 15, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 891) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl) `ZINC001626501006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626501006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626501006 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(C)(C)Oc3ccc(C(F)(F)F)cc32)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 2, 9, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626501006 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626501006 Building ZINC001626513458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626513458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/892 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1) `ZINC001626513458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626513458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626513458 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 15, 12, 15, 15, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 25, 29, 29, 29, 29, 27, 15, 15, 3, 7, 7, 7, 7, 15, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/893 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1) `ZINC001626513458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626513458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626513458 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 14, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 28, 30, 30, 30, 30, 28, 16, 16, 4, 7, 7, 7, 7, 16, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626513458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 Building ZINC001626513458 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626513458 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 892) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1) `ZINC001626513458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626513458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626513458 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 25, 15, 12, 15, 15, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 25, 29, 29, 29, 29, 27, 15, 15, 3, 7, 7, 7, 7, 15, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 893) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1) `ZINC001626513458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626513458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626513458 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1Cl)c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 14, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 28, 30, 30, 30, 30, 28, 16, 16, 4, 7, 7, 7, 7, 16, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626513458 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626513458 Building ZINC001626555905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626555905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/894 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626555905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626555905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626555905 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 25, 29, 29, 27, 27, 29, 29, 29, 29, 29, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 29, 29, 29, 29, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/895 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626555905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626555905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626555905 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 25, 29, 29, 27, 28, 29, 29, 29, 29, 29, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 29, 29, 29, 29, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626555905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 Building ZINC001626555905 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626555905 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 894) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626555905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626555905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626555905 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 25, 29, 29, 27, 27, 29, 29, 29, 29, 29, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 29, 29, 29, 29, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 895) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626555905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626555905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626555905 none O=C(Nc1nnc(Cc2ccc(C(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 6, 6, 25, 29, 29, 27, 28, 29, 29, 29, 29, 29, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 29, 29, 29, 29, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626555905 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626555905 Building ZINC001626596271 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626596271 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/896 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1) `ZINC001626596271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626596271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001626596271 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 41, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/897 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1) `ZINC001626596271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626596271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001626596271 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 6, 6, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626596271 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 Building ZINC001626596271 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626596271 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 896) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1) `ZINC001626596271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626596271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001626596271 none COc1ccc(C2(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 41, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 897) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1) `ZINC001626596271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626596271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001626596271 none COc1ccc(C2(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 27, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 6, 6, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626596271 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626596271 Building ZINC001626615792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626615792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/898 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/899 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/900 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/900' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/901 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/901' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626615792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 Building ZINC001626615792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626615792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 898) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 899) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 900) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 901) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626615792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 Building ZINC001626615792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626615792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 898) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 899) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 900) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 901) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626615792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 Building ZINC001626615792 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626615792 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 898) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 899) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 900) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 901) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C) `ZINC001626615792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626615792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001626615792 none CN1c2ccc(Br)cc2N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 48 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626615792 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626615792 Building ZINC001626747486 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626747486 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/902 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626747486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626747486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626747486 none Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 49, 49, 41, 49, 49, 49, 21, 21, 12, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 49, 49, 41, 49, 49, 49, 49, 21, 21, 21, 12, 12, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/903 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626747486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626747486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626747486 none Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 49, 49, 41, 49, 49, 49, 21, 21, 12, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 49, 49, 41, 49, 49, 49, 49, 21, 21, 21, 12, 12, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626747486 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 Building ZINC001626747486 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626747486 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 902) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626747486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626747486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626747486 none Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 49, 49, 41, 49, 49, 49, 21, 21, 12, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 49, 49, 41, 49, 49, 49, 49, 21, 21, 21, 12, 12, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 903) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626747486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626747486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626747486 none Cc1nn(c2ccccc2C)c(C)c1CN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 49, 49, 41, 49, 49, 49, 21, 21, 12, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 49, 49, 41, 49, 49, 49, 49, 21, 21, 21, 12, 12, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626747486 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626747486 Building ZINC001626839338 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626839338 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/904 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626839338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839338 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 32, 30, 32, 49, 18, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 32, 32, 30, 30, 32, 32, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 4, 3, 3, 3, 3, 32, 32, 32, 32] 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]) total number of confs: 358 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/905 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626839338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839338 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 50, 15, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 3, 3, 3, 3, 29, 29, 29, 29] 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]) total number of confs: 370 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626839338 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 Building ZINC001626839338 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626839338 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 904) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626839338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839338 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 32, 30, 32, 49, 18, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 32, 32, 30, 30, 32, 32, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 4, 3, 3, 3, 3, 32, 32, 32, 32] 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]) total number of confs: 358 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 905) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626839338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839338 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 50, 15, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 3, 3, 3, 3, 29, 29, 29, 29] 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]) total number of confs: 370 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626839338 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839338 Building ZINC001626839339 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626839339 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/906 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839339 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 50, 13, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 29, 29, 28, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 29, 29, 29, 29] 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]) total number of confs: 394 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/907 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839339 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 31, 29, 31, 49, 17, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 31, 31, 30, 30, 31, 31, 31, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 4, 3, 3, 3, 3, 31, 31, 31, 31] 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]) total number of confs: 355 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626839339 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 Building ZINC001626839339 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626839339 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 906) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839339 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 50, 13, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 29, 29, 28, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 29, 29, 29, 29] 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]) total number of confs: 394 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 907) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1) `ZINC001626839339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626839339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001626839339 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 31, 29, 31, 49, 17, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 31, 31, 30, 30, 31, 31, 31, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17, 4, 3, 3, 3, 3, 31, 31, 31, 31] 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]) total number of confs: 355 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626839339 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626839339 Building ZINC001626894234 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626894234 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/908 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626894234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894234 none CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 26, 37, 16, 9, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [51, 25, 54, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/909 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626894234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894234 none CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 29, 43, 17, 12, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626894234 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 Building ZINC001626894234 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626894234 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 908) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626894234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894234 none CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 26, 37, 16, 9, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [51, 25, 54, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 909) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626894234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894234 none CC(C)(C)OC(=O)NCC1([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 29, 43, 17, 12, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626894234 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894234 Building ZINC001626894235 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626894235 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/910 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626894235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894235 none CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 30, 43, 17, 14, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 168 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/911 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626894235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894235 none CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 21, 34, 15, 11, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [51, 25, 54, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626894235 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 Building ZINC001626894235 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626894235 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 910) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626894235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894235 none CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 30, 43, 17, 14, 9, 9, 9, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 17, 17, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 168 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 911) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1) `ZINC001626894235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626894235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001626894235 none CC(C)(C)OC(=O)NCC1([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 21, 34, 15, 11, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [51, 25, 54, 17, 19, 20, 21, 22, 23, 24, 52, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 156 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626894235 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626894235 Building ZINC001626966158 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626966158 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/912 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626966158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966158 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/913 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626966158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966158 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 23, 23, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626966158 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 Building ZINC001626966158 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626966158 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 912) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626966158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966158 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 913) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626966158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966158 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 23, 23, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626966158 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966158 Building ZINC001626966159 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626966159 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/914 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626966159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966159 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 23, 23, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/915 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626966159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966159 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626966159 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 Building ZINC001626966159 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626966159 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 914) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626966159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966159 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 23, 23, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 915) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001626966159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626966159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001626966159 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 68 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001626966159 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001626966159 Building ZINC001627104001 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627104001 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/916 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)c(F)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627104001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627104001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001627104001 none O=C(N1CCc2cc(Br)c(F)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 45 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/917 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)c(F)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627104001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627104001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001627104001 none O=C(N1CCc2cc(Br)c(F)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 47 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627104001 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 Building ZINC001627104001 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627104001 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 916) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)c(F)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627104001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627104001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001627104001 none O=C(N1CCc2cc(Br)c(F)cc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 45 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 917) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)c(F)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627104001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627104001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001627104001 none O=C(N1CCc2cc(Br)c(F)cc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 6] 47 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627104001 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627104001 Building ZINC001627186445 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627186445 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/918 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627186445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627186445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001627186445 none O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 14, 14, 7, 11, 18, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 18, 18, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/919 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627186445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627186445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001627186445 none O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 14, 14, 7, 7, 18, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 18, 18, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627186445 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 Building ZINC001627186445 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627186445 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 918) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627186445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627186445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001627186445 none O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 14, 14, 7, 11, 18, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 18, 18, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 919) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627186445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627186445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001627186445 none O=C(NCc1ccc(Cn2cnc3ccccc32)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 14, 14, 7, 7, 18, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 18, 18, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627186445 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627186445 Building ZINC001627219126 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627219126 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/920 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001627219126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627219126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001627219126 none COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 28, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 49, 49, 8, 8, 2, 2, 1, 2, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/921 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001627219126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627219126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001627219126 none COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 1, 2, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627219126 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 Building ZINC001627219126 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627219126 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 920) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001627219126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627219126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001627219126 none COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 28, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 49, 49, 8, 8, 2, 2, 1, 2, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 921) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001627219126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627219126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001627219126 none COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 1, 2, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627219126 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627219126 Building ZINC001627256009 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627256009 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/922 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21) `ZINC001627256009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627256009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627256009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/923 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21) `ZINC001627256009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627256009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627256009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 5, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627256009 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 Building ZINC001627256009 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627256009 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 922) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21) `ZINC001627256009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627256009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627256009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 923) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21) `ZINC001627256009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627256009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627256009 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 5, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627256009 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627256009 Building ZINC001627316878 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627316878 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/924 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627316878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316878 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 19, 24, 24, 19, 24, 24, 7, 12, 23, 23, 23, 27, 27, 23, 27, 27, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 24, 24, 19, 24, 24, 12, 12, 69, 27, 27, 23, 27, 27, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 269 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/925 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627316878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316878 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 15, 20, 20, 16, 20, 20, 6, 12, 19, 19, 19, 22, 22, 19, 22, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 20, 20, 20, 20, 20, 12, 12, 57, 22, 22, 19, 22, 22, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627316878 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 Building ZINC001627316878 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627316878 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 924) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627316878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316878 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 19, 24, 24, 19, 24, 24, 7, 12, 23, 23, 23, 27, 27, 23, 27, 27, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 24, 24, 19, 24, 24, 12, 12, 69, 27, 27, 23, 27, 27, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 269 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 925) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627316878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316878 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 15, 20, 20, 16, 20, 20, 6, 12, 19, 19, 19, 22, 22, 19, 22, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 20, 20, 20, 20, 20, 12, 12, 57, 22, 22, 19, 22, 22, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627316878 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316878 Building ZINC001627316879 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627316879 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/926 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627316879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316879 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 14, 19, 19, 17, 19, 19, 7, 12, 19, 19, 19, 22, 22, 19, 22, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 19, 19, 19, 19, 19, 12, 12, 57, 22, 22, 19, 22, 22, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/927 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627316879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316879 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 8, 20, 25, 25, 22, 25, 25, 8, 13, 24, 24, 24, 28, 28, 24, 28, 28, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 25, 25, 25, 25, 25, 13, 13, 72, 28, 28, 24, 28, 28, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 274 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627316879 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 Building ZINC001627316879 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627316879 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 926) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627316879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316879 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 14, 19, 19, 17, 19, 19, 7, 12, 19, 19, 19, 22, 22, 19, 22, 22, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 19, 19, 19, 19, 19, 12, 12, 57, 22, 22, 19, 22, 22, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 927) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627316879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627316879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001627316879 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 8, 20, 25, 25, 22, 25, 25, 8, 13, 24, 24, 24, 28, 28, 24, 28, 28, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 25, 25, 25, 25, 25, 13, 13, 72, 28, 28, 24, 28, 28, 3, 1, 3] 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, 44, 45, 46, 47]) total number of confs: 274 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627316879 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627316879 Building ZINC001627318347 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627318347 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/928 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627318347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318347 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 20, 20, 20, 20, 20, 20, 47, 47, 30, 47, 47, 47, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 47, 47, 36, 47, 20, 20, 3, 1, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/929 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627318347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318347 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 10, 16, 16, 16, 16, 16, 16, 47, 47, 28, 47, 47, 47, 16, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 47, 47, 28, 47, 16, 16, 4, 1, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627318347 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 Building ZINC001627318347 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627318347 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 928) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627318347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318347 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 11, 20, 20, 20, 20, 20, 20, 47, 47, 30, 47, 47, 47, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 47, 47, 36, 47, 20, 20, 3, 1, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 929) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627318347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318347 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 10, 16, 16, 16, 16, 16, 16, 47, 47, 28, 47, 47, 47, 16, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 47, 47, 28, 47, 16, 16, 4, 1, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627318347 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318347 Building ZINC001627318348 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627318348 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/930 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627318348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318348 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 10, 16, 16, 16, 16, 16, 16, 46, 46, 21, 46, 46, 46, 16, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 46, 46, 28, 46, 16, 16, 4, 2, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/931 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627318348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318348 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 10, 20, 20, 20, 20, 20, 20, 47, 47, 20, 47, 47, 47, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 47, 47, 33, 47, 20, 20, 3, 1, 3] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627318348 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 Building ZINC001627318348 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627318348 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 930) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627318348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318348 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 10, 16, 16, 16, 16, 16, 16, 46, 46, 21, 46, 46, 46, 16, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 46, 46, 28, 46, 16, 16, 4, 2, 4] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 931) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627318348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627318348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001627318348 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 10, 20, 20, 20, 20, 20, 20, 47, 47, 20, 47, 47, 47, 20, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 20, 20, 47, 47, 33, 47, 20, 20, 3, 1, 3] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627318348 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627318348 Building ZINC001627337120 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627337120 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/932 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627337120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627337120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001627337120 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 7, 15, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/933 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627337120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627337120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001627337120 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 16, 7, 16, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627337120 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 Building ZINC001627337120 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627337120 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 932) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627337120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627337120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001627337120 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 7, 15, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 933) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627337120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627337120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001627337120 none CCOC(=O)c1cc(c2ccccc2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 16, 7, 16, 7, 7, 7, 7, 14, 14, 7, 14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 7, 14, 14, 7, 14, 14, 7, 7, 3, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627337120 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627337120 Building ZINC001627387251 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627387251 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/934 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001627387251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627387251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627387251 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/935 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001627387251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627387251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627387251 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627387251 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 Building ZINC001627387251 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627387251 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 934) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001627387251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627387251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627387251 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 17, 17, 17, 17, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 935) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001627387251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627387251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627387251 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(C)(C)NC(=O)OC(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627387251 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627387251 Building ZINC001627455196 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627455196 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/936 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627455196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455196 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 15, 15, 13, 13, 15, 15, 15, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/937 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627455196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455196 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 9, 9, 9, 9, 9, 5, 12, 12, 10, 10, 12, 12, 12, 4, 4, 4, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627455196 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 Building ZINC001627455196 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627455196 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 936) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627455196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455196 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 15, 15, 13, 13, 15, 15, 15, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 937) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627455196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455196 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 9, 9, 9, 9, 9, 5, 12, 12, 10, 10, 12, 12, 12, 4, 4, 4, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12] 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]) total number of confs: 50 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627455196 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455196 Building ZINC001627455197 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627455197 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/938 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627455197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455197 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 9, 9, 9, 9, 9, 5, 14, 14, 10, 10, 14, 14, 14, 4, 4, 4, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/939 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627455197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455197 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 14, 14, 12, 12, 14, 14, 14, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627455197 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 Building ZINC001627455197 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627455197 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 938) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627455197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455197 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 9, 9, 9, 9, 9, 5, 14, 14, 10, 10, 14, 14, 14, 4, 4, 4, 4, 4, 5, 5, 5, 5, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 939) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001627455197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627455197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001627455197 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)[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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 15, 15, 15, 15, 15, 7, 14, 14, 12, 12, 14, 14, 14, 6, 6, 6, 6, 6, 5, 5, 5, 5, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627455197 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627455197 Building ZINC001627641157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627641157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/940 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F) `ZINC001627641157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627641157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627641157 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 5, 5, 5, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 50, 50, 50, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/941 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F) `ZINC001627641157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627641157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627641157 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 6, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 50, 50, 50, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627641157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 Building ZINC001627641157 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627641157 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 940) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F) `ZINC001627641157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627641157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627641157 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 5, 5, 5, 5, 5, 24, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 50, 50, 50, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 941) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F) `ZINC001627641157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627641157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627641157 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(Oc2ccc(F)c(F)c2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 6, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 50, 50, 50, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 36, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627641157 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627641157 Building ZINC001627901919 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627901919 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/942 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627901919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901919 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 39, 28, 39, 24, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 25, 25, 24, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 12, 12, 3, 3, 1, 3, 25, 25, 24, 25, 25] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/943 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627901919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901919 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 2, 3, 1, 3, 23, 23, 23, 23, 23] 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627901919 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 Building ZINC001627901919 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627901919 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 942) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627901919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901919 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 39, 28, 39, 24, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 25, 25, 24, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 12, 12, 3, 3, 1, 3, 25, 25, 24, 25, 25] 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 943) grep: /scratch/xiaobo/11891/xbl-8058088.38/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)N[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627901919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901919 none CC(C)(C)OC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 2, 3, 1, 3, 23, 23, 23, 23, 23] 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627901919 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901919 Building ZINC001627901920 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627901920 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/944 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901920 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 33, 42, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 9, 9, 2, 3, 1, 3, 23, 23, 23, 23, 23] 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/945 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901920 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 29, 40, 24, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 25, 25, 24, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 12, 12, 3, 3, 1, 3, 25, 25, 24, 25, 25] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627901920 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 Building ZINC001627901920 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627901920 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 944) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901920 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 33, 42, 23, 9, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 9, 9, 2, 3, 1, 3, 23, 23, 23, 23, 23] 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]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 945) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1) `ZINC001627901920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001627901920 none CC(C)(C)OC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 40, 29, 40, 24, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 25, 25, 24, 25, 25, 48, 48, 48, 48, 48, 48, 48, 48, 48, 29, 12, 12, 3, 3, 1, 3, 25, 25, 24, 25, 25] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627901920 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627901920 Building ZINC001627991071 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627991071 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/946 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl) `ZINC001627991071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627991071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627991071 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 20, 20, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/947 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl) `ZINC001627991071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627991071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627991071 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 20, 20, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627991071 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 Building ZINC001627991071 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627991071 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 946) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl) `ZINC001627991071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627991071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627991071 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 20, 20, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 947) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl) `ZINC001627991071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627991071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627991071 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(Cc4ccc(F)cc4)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 20, 20, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627991071 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991071 Building ZINC001627991477 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627991477 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/948 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2ccccc2C(F)(F)F)n1) `ZINC001627991477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627991477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627991477 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 29, 29, 26, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 29, 29, 26, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/949 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2ccccc2C(F)(F)F)n1) `ZINC001627991477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627991477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627991477 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 30, 30, 26, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 30, 30, 26, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627991477 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 Building ZINC001627991477 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627991477 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 948) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2ccccc2C(F)(F)F)n1) `ZINC001627991477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627991477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627991477 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 29, 29, 26, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 29, 29, 26, 29] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 949) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2ccccc2C(F)(F)F)n1) `ZINC001627991477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627991477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001627991477 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 30, 30, 26, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 14, 8, 4, 4, 4, 4, 30, 30, 26, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001627991477 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001627991477 Building ZINC001628036209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628036209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/950 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 43, 43, 43, 43, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/951 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 17, 17, 17, 17, 43, 43, 43, 43, 17, 17, 17, 17, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/952 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/952' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/953 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/953' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628036209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 Building ZINC001628036209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628036209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 950) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 43, 43, 43, 43, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 951) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 17, 17, 17, 17, 43, 43, 43, 43, 17, 17, 17, 17, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 952) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 953) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628036209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 Building ZINC001628036209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628036209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 950) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 43, 43, 43, 43, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 951) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 17, 17, 17, 17, 43, 43, 43, 43, 17, 17, 17, 17, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 952) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 953) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628036209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 Building ZINC001628036209 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628036209 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 950) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 43, 43, 43, 43, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 951) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 17, 17, 17, 17, 43, 43, 43, 43, 17, 17, 17, 17, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 952) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 953) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628036209.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628036209 none O=C(N[C@H]1CC[N@@](c2nc3ccccc3s2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 42, 42, 42, 42, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628036209 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628036209 Building ZINC001628038798 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628038798 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/954 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628038798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038798 none O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 3, 10, 10, 14, 21, 27, 33, 33, 33, 33, 33, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 8, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/955 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628038798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038798 none O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 16, 21, 26, 31, 31, 31, 31, 31, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 11, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628038798 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 Building ZINC001628038798 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628038798 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 954) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628038798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038798 none O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 3, 10, 10, 14, 21, 27, 33, 33, 33, 33, 33, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 10, 8, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 10, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 955) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628038798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038798 none O=C(Nc1cccc(C[S@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 16, 21, 26, 31, 31, 31, 31, 31, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 11, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628038798 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628038798 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038798 Building ZINC001628038799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628038799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/956 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628038799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038799 none O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 3, 11, 11, 16, 22, 26, 30, 30, 30, 30, 30, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 10, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/957 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628038799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038799 none O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 16, 23, 29, 33, 33, 33, 33, 33, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 11, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628038799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 Building ZINC001628038799 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628038799 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 956) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628038799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038799 none O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 3, 11, 11, 16, 22, 26, 30, 30, 30, 30, 30, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 10, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 957) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628038799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628038799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628038799 none O=C(Nc1cccc(C[S@@](=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 16, 23, 29, 33, 33, 33, 33, 33, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 11, 11, 11, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628038799 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628038799 Building ZINC001628077006 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628077006 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/958 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628077006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628077006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001628077006 none O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 25, 34, 34, 34, 34, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 34, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/959 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628077006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628077006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001628077006 none O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 26, 35, 35, 35, 35, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 35, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628077006 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 Building ZINC001628077006 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628077006 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 958) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628077006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628077006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001628077006 none O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 25, 34, 34, 34, 34, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 34, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 959) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628077006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628077006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001628077006 none O=C(Nc1ccc(Sc2nncs2)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 26, 35, 35, 35, 35, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 35, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628077006 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628077006 Building ZINC001628092180 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628092180 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/960 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O) `ZINC001628092180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628092180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628092180 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 5, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 42] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/961 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O) `ZINC001628092180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628092180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628092180 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 5, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 42] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628092180 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 Building ZINC001628092180 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628092180 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 960) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O) `ZINC001628092180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628092180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628092180 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 5, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 42] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 961) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O) `ZINC001628092180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628092180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001628092180 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 21, 5, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 8, 8, 8, 8, 42] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628092180 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628092180 Building ZINC001628115664 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628115664 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/962 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nc(C2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628115664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628115664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001628115664 none O=C(NCCc1nc(C2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 6, 20, 20, 20, 48, 48, 48, 48, 48, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/963 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1nc(C2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628115664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628115664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001628115664 none O=C(NCCc1nc(C2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 6, 21, 21, 23, 48, 48, 48, 48, 48, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 21, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628115664 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 Building ZINC001628115664 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628115664 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 962) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(NCCc1nc(C2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628115664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628115664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001628115664 none O=C(NCCc1nc(C2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 6, 20, 20, 20, 48, 48, 48, 48, 48, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 963) grep: /scratch/xiaobo/11891/xbl-8058088.38/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(NCCc1nc(C2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628115664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628115664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001628115664 none O=C(NCCc1nc(C2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 6, 21, 21, 23, 48, 48, 48, 48, 48, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 2, 5, 5, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 21, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628115664 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628115664 Building ZINC001628283878 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628283878 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/964 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC001628283878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628283878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628283878 none Cc1csc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 3, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 35, 35, 35, 35, 35, 23, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/965 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC001628283878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628283878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628283878 none Cc1csc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 35, 35, 35, 35, 35, 18, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628283878 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 Building ZINC001628283878 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628283878 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 964) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1csc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC001628283878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628283878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628283878 none Cc1csc(Nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 3, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 35, 35, 35, 35, 35, 23, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 965) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: Cc1csc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1) `ZINC001628283878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628283878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628283878 none Cc1csc(Nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 4, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 35, 35, 35, 35, 35, 18, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628283878 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628283878 Building ZINC001628307770 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307770 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/966 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/967 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/968 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/968' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/969 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/969' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307770 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 Building ZINC001628307770 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307770 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 966) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 967) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 968) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 969) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307770 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 Building ZINC001628307770 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307770 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 966) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 967) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 968) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 969) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307770 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 Building ZINC001628307770 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307770 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 966) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 967) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 26, 26, 26, 26, 26, 26, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 131 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 968) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 969) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307770.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307770 none CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307770 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307770 Building ZINC001628307772 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307772 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/970 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/971 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/972 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/972' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/973 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/973' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307772 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 Building ZINC001628307772 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307772 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 970) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 971) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 972) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 973) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307772 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 Building ZINC001628307772 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307772 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 970) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 971) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 972) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 973) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307772 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 Building ZINC001628307772 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628307772 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 970) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 971) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 10, 16, 25, 25, 25, 25, 25, 25, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 10, 10, 16, 16, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `2' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 2 (index: 972) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `3' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 3 (index: 973) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628307772.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628307772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001628307772 none CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 3, 7, 12, 20, 20, 20, 20, 20, 20, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628307772 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 3: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/3.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/0.* 2: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772/2.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628307772 Building ZINC001628330555 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628330555 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/974 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1) `ZINC001628330555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628330555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001628330555 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 13, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 40, 40, 34, 34, 40, 40, 40, 40, 40, 40, 40, 13, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40] 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: 199 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/975 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1) `ZINC001628330555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628330555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001628330555 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 13, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 39, 39, 22, 22, 39, 39, 40, 40, 40, 40, 40, 13, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39] 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: 245 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628330555 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 Building ZINC001628330555 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628330555 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 974) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1) `ZINC001628330555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628330555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001628330555 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 13, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 40, 40, 34, 34, 40, 40, 40, 40, 40, 40, 40, 13, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40] 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: 199 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 975) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1) `ZINC001628330555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628330555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001628330555 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)[nH]nc1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 6, 8, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 13, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 22, 22, 39, 39, 22, 22, 39, 39, 40, 40, 40, 40, 40, 13, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39] 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: 245 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628330555 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628330555 Building ZINC001628341114 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628341114 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/976 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628341114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628341114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628341114 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/977 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628341114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628341114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628341114 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628341114 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 Building ZINC001628341114 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628341114 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 976) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628341114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628341114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628341114 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 977) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628341114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628341114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628341114 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628341114 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628341114 Building ZINC001628360610 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628360610 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/978 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1) `ZINC001628360610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628360610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628360610 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 3, 10, 18, 18, 18, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 10, 18, 10, 10, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40] set([0, 1, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/979 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1) `ZINC001628360610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628360610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628360610 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 6, 10, 19, 19, 19, 10, 10, 10, 10, 11, 11, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 10, 19, 10, 11, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40] set([0, 1, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628360610 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 Building ZINC001628360610 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628360610 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 978) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1) `ZINC001628360610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628360610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628360610 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 3, 10, 18, 18, 18, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 10, 18, 10, 10, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40] set([0, 1, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 979) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1) `ZINC001628360610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628360610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628360610 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(OC(F)F)cc2OC(F)F)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 6, 10, 19, 19, 19, 10, 10, 10, 10, 11, 11, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 10, 10, 19, 10, 11, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 40] set([0, 1, 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, 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/11891/xbl-8058088.38/working/building/ZINC001628360610 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628360610 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628360610 Building ZINC001628375546 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628375546 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/980 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628375546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375546 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 20, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 33, 35, 35, 35, 35, 35, 35, 20, 20, 20, 13, 13, 3, 4, 4, 4, 4, 35, 35, 35, 35] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/981 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628375546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375546 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 32, 34, 34, 34, 34, 34, 34, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628375546 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 Building ZINC001628375546 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628375546 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 980) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628375546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375546 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 20, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 33, 35, 35, 35, 35, 35, 35, 20, 20, 20, 13, 13, 3, 4, 4, 4, 4, 35, 35, 35, 35] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 981) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628375546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375546 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 32, 34, 34, 34, 34, 34, 34, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628375546 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375546 Building ZINC001628375547 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628375547 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/982 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628375547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375547 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 32, 34, 34, 32, 32, 34, 34, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/983 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628375547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375547 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 34, 35, 35, 35, 35, 35, 35, 21, 21, 21, 14, 14, 3, 4, 4, 4, 4, 35, 35, 35, 35] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628375547 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 Building ZINC001628375547 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628375547 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 982) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628375547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375547 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 32, 34, 34, 32, 32, 34, 34, 21, 21, 21, 15, 15, 3, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 983) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1) `ZINC001628375547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628375547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001628375547 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)Sc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 34, 35, 35, 35, 35, 35, 35, 21, 21, 21, 14, 14, 3, 4, 4, 4, 4, 35, 35, 35, 35] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628375547 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628375547 Building ZINC001628493077 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628493077 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/984 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628493077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493077 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [46, 46, 46, 46, 39, 29, 39, 29, 29, 29, 8, 29, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 29, 29, 4, 3, 1, 3, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/985 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628493077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493077 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [44, 44, 44, 44, 39, 28, 39, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 44, 44, 44, 44, 44, 44, 44, 44, 44, 28, 28, 28, 28, 4, 3, 1, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628493077 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 Building ZINC001628493077 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628493077 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 984) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628493077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493077 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [46, 46, 46, 46, 39, 29, 39, 29, 29, 29, 8, 29, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 29, 29, 4, 3, 1, 3, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 985) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628493077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493077 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [44, 44, 44, 44, 39, 28, 39, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 44, 44, 44, 44, 44, 44, 44, 44, 44, 28, 28, 28, 28, 4, 3, 1, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628493077 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493077 Building ZINC001628493078 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628493078 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/986 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628493078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493078 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 40, 28, 40, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 28, 28, 28, 28, 4, 3, 1, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/987 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628493078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493078 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 42, 42, 42, 37, 23, 37, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 4, 3, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628493078 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 Building ZINC001628493078 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628493078 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 986) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628493078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493078 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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: [45, 45, 45, 45, 40, 28, 40, 28, 28, 28, 8, 28, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 45, 45, 45, 45, 45, 45, 45, 45, 45, 28, 28, 28, 28, 4, 3, 1, 3, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 987) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2) `ZINC001628493078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628493078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001628493078 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC12CCC2 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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 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, 42, 42, 42, 37, 23, 37, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 4, 3, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [13, 16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628493078 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628493078 Building ZINC001628500182 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628500182 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/988 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/988' -> `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](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628500182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500182 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 21, 21, 30, 41, 41, 50, 50, 50, 50, 21, 24, 24, 21, 21, 34, 34, 24, 24, 2, 2, 2, 2, 2, 2, 4, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 34, 34, 34, 34, 34, 34, 34, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/989 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/989' -> `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](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628500182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500182 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 25, 40, 40, 47, 47, 47, 47, 17, 23, 23, 18, 23, 28, 29, 23, 23, 2, 2, 2, 2, 2, 2, 3, 11, 11, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628500182 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 Building ZINC001628500182 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628500182 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 988) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628500182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500182 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 21, 21, 30, 41, 41, 50, 50, 50, 50, 21, 24, 24, 21, 21, 34, 34, 24, 24, 2, 2, 2, 2, 2, 2, 4, 12, 12, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 34, 34, 34, 34, 34, 34, 34, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 989) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628500182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500182 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 17, 17, 25, 40, 40, 47, 47, 47, 47, 17, 23, 23, 18, 23, 28, 29, 23, 23, 2, 2, 2, 2, 2, 2, 3, 11, 11, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 23, 29, 29, 29, 29, 29, 29, 29, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628500182 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500182 Building ZINC001628500183 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628500183 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/990 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/990' -> `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](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628500183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500183 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 18, 18, 26, 43, 43, 46, 46, 46, 46, 18, 24, 24, 23, 23, 33, 33, 24, 24, 2, 2, 2, 2, 2, 2, 3, 11, 11, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/991 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/991' -> `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](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628500183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500183 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 21, 21, 29, 40, 40, 50, 50, 50, 50, 21, 24, 24, 24, 24, 34, 34, 24, 24, 2, 2, 2, 2, 2, 2, 4, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 34, 34, 34, 34, 34, 34, 34, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628500183 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 Building ZINC001628500183 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628500183 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 990) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628500183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500183 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 18, 18, 26, 43, 43, 46, 46, 46, 46, 18, 24, 24, 23, 23, 33, 33, 24, 24, 2, 2, 2, 2, 2, 2, 3, 11, 11, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 33, 33, 33, 33, 33, 33, 33, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 991) grep: /scratch/xiaobo/11891/xbl-8058088.38/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)cc1) `ZINC001628500183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628500183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001628500183 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)OC(C)(C)C)c1ccc(C(C)C)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 12, 21, 21, 29, 40, 40, 50, 50, 50, 50, 21, 24, 24, 24, 24, 34, 34, 24, 24, 2, 2, 2, 2, 2, 2, 4, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 34, 34, 34, 34, 34, 34, 34, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628500183 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628500183 Building ZINC001628527351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628527351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/992 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628527351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527351 none C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 31, 32, 32, 32, 32, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/993 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628527351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527351 none C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 13, 22, 33, 33, 33, 33, 33, 33, 3, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 3, 4, 4, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628527351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 Building ZINC001628527351 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628527351 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 992) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628527351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527351 none C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 31, 31, 32, 32, 32, 32, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 993) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628527351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527351 none C[C@@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 13, 22, 33, 33, 33, 33, 33, 33, 3, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 3, 4, 4, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628527351 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527351 Building ZINC001628527352 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628527352 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/994 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628527352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527352 none C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 32, 35, 35, 35, 35, 12, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 3, 4, 4, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/995 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628527352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527352 none C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 20, 30, 30, 33, 33, 33, 33, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628527352 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 Building ZINC001628527352 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628527352 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 994) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628527352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527352 none C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 32, 35, 35, 35, 35, 12, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 3, 4, 4, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 995) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001628527352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628527352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628527352 none C[C@H](NC(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 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, 6, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 11, 20, 30, 30, 33, 33, 33, 33, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628527352 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628527352 Building ZINC001628560682 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628560682 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/996 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628560682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560682 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [8, 2, 5, 6, 7] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: 56 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/997 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628560682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560682 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 55 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628560682 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 Building ZINC001628560682 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628560682 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 996) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628560682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560682 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [8, 2, 5, 6, 7] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: 56 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 997) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628560682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560682 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 15, 15, 17, 17, 17, 17, 17, 17, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 55 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628560682 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560682 Building ZINC001628560683 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628560683 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/998 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628560683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560683 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2] 50 rigid atoms, others: [8, 2, 5, 6, 7] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/999 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628560683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560683 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 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: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628560683 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 Building ZINC001628560683 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628560683 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 998) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628560683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560683 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 17, 17, 17, 17, 17, 17, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2] 50 rigid atoms, others: [8, 2, 5, 6, 7] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 mkdir: created directory `1' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 1 (index: 999) grep: /scratch/xiaobo/11891/xbl-8058088.38/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1) `ZINC001628560683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628560683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628560683 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2CCCCCN2C(=O)Nc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3] 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: 64 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628560683 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 1: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/1.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628560683 Building ZINC001628661952 mkdir: created directory `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001628661952 mkdir: created directory `0' /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952/0 /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/11891/xbl-8058088.38/working/3D/1000 `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001628661952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628661952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001628661952 none O=C(Nc1ccc(OCc2ccccc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 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: [2, 1, 2, 2, 7, 7, 7, 7, 20, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 2, 2, 4, 2, 2] 100 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952 /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Finished preparing ZINC001628661952 Recording results /scratch/xiaobo/11891/xbl-8058088.38/working /scratch/xiaobo/11891/xbl-8058088.38 Appending to /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.* 0: /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952/0.* Removing working files in /scratch/xiaobo/11891/xbl-8058088.38/working/building/ZINC001628661952 /scratch/xiaobo/11891/xbl-8058088.38 Compressing combined databse files /scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/11891/xbl-8058088.38/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/11891/xbl-8058088.38/working/3D/1001' removed directory: `/scratch/xiaobo/11891/xbl-8058088.38/working/3D' rmdir: removing directory, `/scratch/xiaobo/11891/xbl-8058088.38/working/building' rmdir: removing directory, `/scratch/xiaobo/11891/xbl-8058088.38/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/11891/xbl-8058088.38' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbl' `/scratch/xiaobo/11891/xbl-8058088.38/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbl/finished' `/scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbl/finished/xbl.db2.gz' removed `/scratch/xiaobo/11891/xbl-8058088.38/finished/xbl.db2.gz' removed directory: `/scratch/xiaobo/11891/xbl-8058088.38/finished' removed directory: `/scratch/xiaobo/11891/xbl-8058088.38'